SeekSoulOnline Release Notes

Author: SeekGene

Time: 31 min

Words: 6.2k words

Updated: 2025-11-07

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V5.5.2.250903

What's New:
I. System

1.1 When using email verification, send the verification code to the email bound to the username rather than the username itself (because some usernames are not email addresses, which previously caused delivery failures);

1.2 In both the Chinese and English versions, hide the phone-number field once Email is selected as the verification method.

1.3 Replace the company logo with the English version and refine the English UI workflow and presentation.

V5.5.1.250806

Release Date: August 6, 2025

What's New:
I. Resource Overview

【My Data】: Improve the loading speed of the My Data list; add matrix and raw matrix files for _GE samples in scATAC products.

【Analysis Workflows】: Fix the bug encountered when copying workflows.

【Analysis Workflows – Advanced Analysis】: Restrict the TCR grouping-factor parameter so that Sample cannot be selected; make the Monocle2 filtering factor and filtering target required fields.

II. System

1. SeekSoulOnline now supports language switching between Chinese and English.

V5.4.1.250625

Release Date: June 25, 2025

What's New:
I. Resource Overview

【My Databases】 and 【My Gene Sets】: Add databases for several non-model species.

【My Projects – Analysis Workflows】:

• When reclaiming an instance, add synchronized snapshot saving.
• When deleting a project or workflow, also delete the subset data generated by that workflow and any workflows created from that subset.
• Subset tissues inherit the tissue of the parent cluster.
• Record cell annotation, Differential Enrichment, and Feature Analysis summaries, as well as deletion logs in Result Overview.
• Optimize asynchronous interfaces.
• Improve workflow copying.

【Analysis Workflows – Basic Analysis】:

• Speed up seekARC data initialization and storage.
• Refine global-parameter retrieval logic after initialization.
• Recommend RPCA as a replacement for CCA.

【Analysis Workflows – Plotting Tool】: Optimize data size for violin plots, DimPlot, and FeaturePlot.

【Analysis Workflows – Differential Enrichment】: Support aggregating multiple comparison schemes during 【Summary】; add a new 【Abort】 action to stop Differential Enrichment jobs; optimize volcano plots.

【Analysis Workflows – Advanced Analysis】:

• Auto-fill sample-information parameters for mut, rMAST, Fusion, and lncCoExpression.
• Remove the species parameter from ATAC_Peak2Gene.
• Remove the downsample and downsample_num fields from the CytoTRACE page.

【Analysis Workflows – Auxiliary Information】: Merge subset annotations in meta.data and merge columns in merge.metadata.

II. System

【Login】: Improve the prompts shown when changing passwords.

【Home – Library】: Allow downloading Jupyter templates from the template library.

V5.3.1.250529

Release Date: May 29, 2025

What's New:
I. Resource Overview

【My Data】: Add columns for contract ID and workflow members (admin permission); add a data-linking feature (channel admin permission).

【Analysis Workflows】: Add a summary list in the lower-right corner to record all summaries for the workflow; fix the issue where grouped subsets failed to use Sample after initialization; improve workflow startup and shutdown speed.

【My Data – Data Upload】: Add validation to determine whether an OBJ file supports downsampling.

【Analysis Workflows – Basic Analysis】: Optimize violin plots after initialization and filtering; add statistics for the number of selected datasets.

【Analysis Workflows – Cell Annotation】: After running SingleR or SingleR + AI annotation, prevent renaming the grouping; add the ability to download the annotation table.

【Analysis Workflows – Plotting Tool】: Optimize plotting data for dimensionality reduction plots, FeaturePlot, and violin plots; enhance grouped heatmaps with group layout support.

【Analysis Workflows – Differential Enrichment】: Display task IDs for differential and enrichment jobs.

【Analysis Workflows – Interactive Analysis】: After segmentation, sample labels now only allow letters, numbers, underscores, and spaces, and must start with a letter or number.

【Analysis Workflows – Result Overview】: Improve retrieval of fastp reports in cloud analysis summaries.

【Analysis Workflows – Advanced Analysis】:

• scVelo: Support bulk uploading of loom files (sampleName.loom in ZIP archives).
• BCR/TCR: Allow the calculation method and grouping factor to coexist.
• Add CopyscAT, ataCNV, epiAneufinder, ATAC_Monocle3, rMATs, Fusion, mut, and LncCoExpression advanced analyses.
• Introduce the processType parameter to streamline advanced analysis and support seekARC datasets.

II. System

【Home】: Allow email or phone verification when logging in or registering.

V5.2.1.250415

Release Date: April 15, 2025

What's New:
I. Resource Overview

【Sample Projects】: Add a new ARC (PBMC sample) example project;

【My Data – Data Upload】: Support standard-analysis RDS files whose meta.data lacks a Sample column;

【My Projects – Analysis Workflows】: When copying a workflow, also copy GSEA result plots and the regulon.txt/meta.txt files from Advanced Analysis;

【Analysis Workflows – Cell Annotation】: When performing AI annotation, allow users to input tissue information for the AI step;

【Analysis Workflows – Plotting Tool】: Add an option in the toolbar to place the legend on the right;

【Analysis Workflows – Enrichment Analysis】: Improve the naming of downloaded differential gene tables and enrichment tables;

【Analysis Workflows – Advanced Analysis】: Remove export-parameter buttons when rerunning scenic, monocle2, GSVA, and group_diffenrich based on historical analyses;

• DiffEnrich: Add an “others” species option that limits the workflow to differential analysis only;
• scVelo: Remove the species parameter;
• Add the CellCharter, SpaGene, cellphonedb_spatial, COMMOT, and MISTy spatial modules;
• Restrict the lambda range for Banksy_SpatialClustering to 0–1;

V5.2.1.250320

Release Date: March 20, 2025

What's New:
I. Resource Overview

【My Projects – Personalized Analysis】: Mount three storage locations—BACKUP (OSS), /PROJ2/FLOAT/user, and project (NAS)—so users can analyze data under project; add a 【Mount】 button to reattach or detach storage for active Jupyter sessions; refine permissions;

【My Projects – Analysis Workflows】: When using 【Copy】, duplicate the workflow type as well;

【Analysis Workflows – Basic Analysis】: Add RPCA as an RNA integration method; allow group or sample names that begin with numbers during initialization;

【Analysis Workflows – Plotting Tool】: In the Add Plot Group dialog, add an auto-layout option for gene-set plotting to visualize all genes in a set or the scoring results;

【Analysis Workflows – Enrichment Analysis】: Add ES peak plots to all Differential Enrichment outputs that use GSEA; allow selecting a pathway to redraw the plot; let grouping support numeric prefixes; sort GSEA bubble and bar charts by the absolute NES value; when generating custom ORA or GSEA bubble/bar charts, display the full enrichment table in the popup; add presto as a statistical method; include average expression columns in differential tables;

【Analysis Workflows – Advanced Analysis】:

• stlearn: Allow only one selection for the filtering target and add a cell-type parameter;
• infercnv: Enforce a minimum average expression ≥ 0.01;
• CellChat_spatial: Optimize CellChat analysis for seekSpace data;
• Remove the analysis-type parameter from monocle3, infercnv, scenic, monocle2, DiffEnrich, CytoTRACE, CellChat, scMetabolism, scVelo, scoring, group_diffenrich, Augur, and hdWGCNA;
• ATAC_DiffEnrich: Introduce gene and peak differential analysis for ATAC datasets;
• GeneActivity: Add gene activity analysis for ATAC datasets;
• Add the cloneType calculation method (ct) parameter, defaulting to Sample;

II. System

【Smart Consultation】: Enhance PC and mobile logic, UI styling, responses, and features; remove the Online Consultation button and move the action to the Smart Assistant AI reply; mobile link: https://xunxiaoyin.seekgene.com/#/mobileChat

V5.2.1.250226

Release Date: February 26, 2025

What's New:
I. Resource Overview

【Analysis Workflows – Differential Enrichment】: Sort GSEA results by the NES column in descending order; add Presto as a differential-analysis option to accelerate processing; include average-expression columns in differential tables.

V5.1.1.250218

Release Date: February 18, 2025

What's New:
I. Resource Overview

【Analysis Workflows – Data Upload】: For standard-analysis results, validate that uploaded file names contain only letters, numbers, and underscores.

【Analysis Workflows – Cell Annotation】: Introduce the SingleR + AI mode (combining SingleR output with cluster top-20 genes interpreted via LLMs, with manual review); rename the rat reference from ref_Mouse_all to ref_Rat_all.

【Analysis Workflows – Enrichment Analysis】: Append database identifiers to enrichment-figure names in reports.

【Analysis Workflows – Advanced Analysis】: Add the processType parameter to control which advanced analyses are available (e.g., scRNA, scRNA + VDJ).

• BCR, TCR, scVelo: add resume/unfreeze capability.
• float task names now include project ID, workflow ID, and advanced-analysis ID.
• Support environments located under the jp_envs path.

II. System

【Smart Consultation】: Leverage the SeekSoulOnline database to answer experimental, bioinformatics, and platform questions via the Smart Consultation button (lower-right corner).

V5.1.1.250116

Release Date: January 16, 2025

What's New:
I. Resource Overview

【Analysis Workflows – Basic Analysis】: Restrict the 【Group】 field to letters, numbers, and underscores (must start with a letter); clarify the “skip filtering” prompt.

【Analysis Workflows – Plotting Tool】: Add options in the violin-plot toolbar to show inner boxplots and mean lines.

【Analysis Workflows – Differential Enrichment】: Show control groups before experimental groups in violin/heatmap outputs and refine font sizes.

【Analysis Workflows – Advanced Analysis】:

• Add hdWGCNA.
• monocle3: require the downsample parameter.
• CellChat: make grouping and filtering factors mutually exclusive; rename filtering factor to “Group Comparison” and filtering target to “Comparison Target”; require at least two cell types and add a “Delete All” button.
• NicheNet: make grouping factors mutually exclusive with comparisons.
• Remove 10X_Visium from the analysis-type dropdown for monocle3, infercnv, scenic, monocle2, DiffEnrich, CytoTRACE, scMetabolism, scVelo, scoring, and group_diffenrich.

【Analysis Workflows – Auxiliary Information】: Add a format-conversion tool that casts metadata columns to character or numeric types; prevent deleting or editing the raw_Sample column.

V5.1.1.250102

Release Date: January 2, 2025

What's New:
I. Resource Overview

【Analysis Workflows – Basic Analysis】: Fix the issue where spatial samples could not change the Sample field during initialization.

【Analysis Workflows – Cell Annotation】: Keep at least one resolution result in the resolution list; compute fold change using all genes; convert the add-resolution feature to an asynchronous interface; allow exact search in the gene column; support annotation and visualization for combined ATAC and RNA multi-omics results.

【Analysis Workflows – Plotting Tool】: Support visualizing dimensionality-reduction results for ATAC data.

【Analysis Workflows – Differential Enrichment】: Lower the minimum differential gene threshold to 0.001.

【Analysis Workflows – Interactive Analysis】: Add ATAC peak plots and support ATAC dimensionality-reduction visualization.

【Analysis Workflows – Advanced Analysis】: Add the Augur analysis module to pinpoint cell populations that respond earliest to experimental conditions.

【Analysis Workflows – Auxiliary Information】: Improve validation for metadata, upload-and-merge meta, and duplicate-column features to protect SeekSoulOnline-specific fields; merge parent-cluster labels into subset entries in meta.data without introducing NAs.

II. System

【Library】: Add advanced-analysis videos for SeekSoulOnline.

【Login Page】: Refine the messaging that prompts users to log in again.

【AI Assistant】: Introduce an AI helper for cell markers.

【marker】: Allow precise search in the Cell_Marker column.

V4.4.1.241219

Release Date: December 19, 2024

What's New:
I. Resource Overview

【Parameter Templates】: Add ATAC-specific templates; expand the SeekGene Recommended, SeekSpace, and ATAC templates with mitochondrial gene-set filtering (threshold 0–20).

【Analysis Workflows – Basic Analysis】: Support SeekGene scATAC basic analysis (single-sample and multi-sample integration).

【Analysis Workflows – Cell Annotation, Feature Analysis, Plotting Tool, Differential Enrichment, and Interactive Analysis】: Restrict input fields to prevent entering gene names or other special characters.

【Analysis Workflows – Advanced Analysis】:

• NicheNet: make <Treatment> and <Control> mutually exclusive.
• TCR, BCR, and scVelo: add handling for missing data (contact sales to release data during upload); refine parameter inspection for TCR and BCR; add a sub_celltype factor type for BCR so specific subsets can be analyzed.
• monocle3: add a downsample parameter with a default value of False.

II. System

【Learning Center】: Add database resources to the Learning Center.

V4.4.1.241204

Release Date: December 4, 2024

What's New:
I. Resource Overview

【Parameter Templates】: Remove cluster resolution 0.8 and PCA dimension 30 from the SeekGene Recommended and SeekSpace templates; expand the SeekGene Recommended color palette to 60 colors.

【Analysis Workflows】: Fix the bug where simultaneous mass 【Start】 actions caused failures; add a celltaxonomy database marker table and allow creating gene sets from it.

【Analysis Workflows – Basic Analysis】: Add a cold-storage detection prompt during 【Initialization】; support datasets with ≤60 clusters.

【Analysis Workflows – Plotting Tool】: Fix duplicate legend/title issues; hide sample-integration dimensionality labels in cloud analysis outputs.

【Analysis Workflows – Differential Enrichment】: Reduce the number of genes plotted in volcano, heatmap, and violin charts from 50 to 20; extend enrichment parameter notes with the list of species supported by SeekSoulOnline.

【Analysis Workflows – Result Overview】: Refine spatial report titles, descriptions, footnotes, and captions; add experimental procedures and method content.

【Analysis Workflows – Auxiliary Information】: In Tag Management, add upload-and-merge meta and duplicate-column utilities.

【Analysis Workflows – Advanced Analysis】: Improve Diffenrich annotations; shorten infercnv and monocle2 runtimes; default GSVA to downsample.

V4.4.1.241120

Release Date: November 20, 2024

What's New:
I. Resource Overview

【My Projects】: Fix the bug where both project owners and members could not search for the project.

【My Data】: SeekSpace now links only to standard-analysis results.

【My Data – Data Upload】: Add prompts when deleting samples; synchronize expiration dates for uploaded data when a user account is deactivated or extended.

【My Workflows – Basic Analysis】: Sort grouping lists by sample name.

【Analysis Workflows – Cell Annotation】: When deleting resolution results on the page, remove the corresponding files as well.

【Analysis Workflows – Plotting Tool】: Enable three auto-layout modes (bioinformatics/technical permission) to automate report figures; add an expression-threshold option to dot plots; add a vector-graphics parameter (default off) for dimensionality-reduction and FeaturePlot outputs.

【Analysis Workflows – Feature Analysis】: Add prebuilt rat gene sets.

【Analysis Workflows – Differential Enrichment】: When deleting comparison schemes, also delete the related files; default to the first comparison pair; completed comparisons can only view parameters and cannot be resubmitted; add a warning when downsample = No.

【Analysis Workflows – Result Overview】: Refine header text in reports.

【Analysis Workflows – Advanced Analysis】: Optimize CellChat results.

II. System

【Login Page】: Improve login-page messaging.

【Profile】: Require verification codes when changing passwords or phone numbers.

V4.4.1.241106

Release Date: November 6, 2024

What's New:
I. Resource Overview

【Analysis Workflows – Personalized Analysis】: Allow code-based analysis of SeekSoulOnline outputs (internal permission only).

• Template Library: Add a library where .ipynb files can be uploaded to private or public repositories, with delete support; users can pull templates and preview them directly from Home → Library (Analysis/Documents).
• Jupyter Link: Add a 【Details】 button in the data-analysis list to jump to the Jupyter page.
• Reset Resources: Let users request computing nodes; if a Jupyter session is active, close the current node before opening a new one.
• Get Link: Provide OSS file addresses or push results to the corresponding LIMS batch.
• Aggregate Results: Use 【Aggregate】 to collect files under Result Overview → Personalized Analysis.
• Log Management: Track Personalized Analysis logs and usage fees.

【Analysis Workflows – Auxiliary Information】: Show only workflows from the current project in the meta.data list.

【Analysis Workflows – Advanced Analysis】: Add Banksy_SpatialClustering (see Advanced Analysis FAQ Q9 for details).

II. System

【Data Deletion】:

• Sample projects: auto-delete 30 days after retrieval (send a reminder email 7 days prior so users can download data).
• Workflow purge: delete database and OSS files 30 days after a workflow is removed from the UI (including the sample-project workflows above).

V4.4.1.241016

Release Date: October 16, 2024

What's New:
I. Resource Overview

【Parameter Templates】: Set differential analysis to skip downsampling by default; add p_val as a differential criterion.

【Analysis Workflows – Differential Enrichment】:

• Comparison Schemes: add progress tracking; fix the bug where you could not reorder comparison pairs after searching while creating a scheme.
• Tables: display the type column in differential-analysis tables; default enrichment tables to count sorting; clicking a GO/KEGG term shows the gene-set ID.
• Visualizations: reorder volcano-plot legends (up/down/no-sig); add enrichment bar charts; optimize downloaded file names (scheme_celltype_comparison_direction_tableType/figureType).
• Parameters: default log2FC to 0; add global GO options and plotting.

【Analysis Workflows – Advanced Analysis】: Add an analysis-batch dropdown for BCR and TCR to select result files by batch and remove path information.

V4.4.1.240912

Release Date: September 12, 2024

What's New:
I. Resource Overview

【My Projects】: Customize project lists with contract ID, contract name, and description fields.

【Analysis Workflows – Basic Analysis】: Fix the bug where workflows failed to restart after filtering.

【Analysis Workflows – Interactive Analysis】: Support multi-sample displays.

【Analysis Workflows – Advanced Analysis】:

• BCR and TCR: add bulk upload configuration.
• GSVA: introduce a downsample parameter; limit selections to one gene set.
• scenic: improve the Regulon dropdown based on the historical-task-name parameter.
• scMetabolism: remove gsva and ssgsea as analysis methods.

II. System

【Home Page】: Launch a SeekSoulOnline homepage featuring announcements, the library (learning videos, analysis code, demo data, etc.), project articles, and user profiles.

V4.4.1.240821

Release Date: August 21, 2024

What's New:
I. Resource Overview

【My Data – Data Upload】: Allow batch uploads (bioinformatics and channel permissions); align data expiration with the account; when deleting uploaded data, retain the upload record but remove the data.

【My Projects – Analysis Workflows】: Improve RDS uploads so that built-in resolutions are recognized.

【Analysis Workflows – Cell Annotation】: Replace hyphens (-) with underscores (_) in reference cell names.

【Analysis Workflows – Plotting Tool】: Add AI-assisted plotting; enhance timeout warnings when too many genes are plotted.

【Analysis Workflows – Advanced Analysis】: Add downsample parameters to CytoTRACE and copyKAT.

II. System

【Color Schemes】: Allow multiple color options for continuous palettes.

【User Management】: Contract users for standard and cloud analysis projects can access all modules, while QC project users are limited to Basic Analysis, Cell Annotation, Plotting Tool, Interactive Analysis, and Result Overview.

V4.4.1.240731

Release Date: July 31, 2024

What's New:
I. Resource Overview

【My Projects – Analysis Workflows】: Add an “Updated At” column and sort workflows by update time.

【My Data】: Calculate and display cell counts based on standard-analysis and uploaded data; default to 10,000 cells per sample if historical data is missing.

【Analysis Workflows – Basic Analysis】: Optimize the structure of My Databases and My Gene Sets.

【Analysis Workflows – Cell Annotation】: Improve x-axis ordering for gene-set plots; replace / with _or_ and + with spaces in reference cell-type names.

【Analysis Workflows – Plotting Tool】: Sort group-factor and split-factor labels alphabetically or numerically.

【Analysis Workflows – Differential Enrichment】: Allow parameter inspection for in-progress tasks.

【Analysis Workflows – Advanced Analysis】: Add parameter-import functionality to reuse settings from historical tasks; require at least one cell type in CellphoneDB; convert scenic’s regulon parameter to a dropdown to enable secondary analysis.

【Analysis Workflows – Auxiliary Information】: Prompt users to select an online parent workflow before choosing a subset workflow on the meta.data page.

II. System

【Parameter Templates】: Filter by gene-set expression using a range method; change the default threshold to 0–10.

V4.4.1.240717

Release Date: July 17, 2024

What's New:
I. System

【User Management】: Add roles and permissions for channel admins, channel users, and channel sub-users. Channel admins and sub-users are peers and can create users, allocate upload quotas, and respond to inquiries.

V4.4.1.240710

Release Date: July 10, 2024

What's New:
I. Resource Overview

【My Data – Data Upload】: Add an uploader field.

【Analysis Workflows – Plotting Tool】: Add sorting options to pie charts so they follow group-factor order.

【Analysis Workflows – Differential Enrichment】: Record completion times for comparison schemes.

【Analysis Workflows – Advanced Analysis】: In the 【View】 pane for scVelo, TCR, and BCR, add delete buttons; remove filtering-factor and filtering-target parameters from scVelo; optimize advanced-analysis data storage.

【Analysis Workflows – Personalized Analysis】: Add a template database to upload and download Jupyter templates.

II. System

【Configuration Management】: Improve image storage handling.

【Sample Projects】: Replace the spatial sample project with sample 1092.

V4.4.1.240626

Release Date: June 26, 2024

What's New:
I. Resource Overview

【Analysis Workflows – Basic Analysis】: Add snapshot saving when a basic analysis finishes.

【Analysis Workflows – Differential Enrichment】: Default to displaying all differential results first; ensure repeated GSEA runs yield consistent results; synchronize ordering between aggregated bar/heat/violin plots in the interactive view.

【Analysis Workflows – Auxiliary Information】: Add a “Workflow ID” column to the meta.data list.

【Analysis Workflows – Advanced Analysis】:

• Add an “Analysis Completed Time” column and email notifications after advanced analyses finish.
• Introduce two new analyses: scoring and group_diffenrich.
• Refine Monocle state parameter settings.
• Tweak scVelo parameters.
• For copyKAT and scVelo, rename split factor/object to filtering factor/object.
• Update analysis-type options for Diffenrich, monocle3, CytoTRACE, infercnv, scMetabolism, and scVelo.
• Add rat as a supported species in infercnv.

【Analysis Workflows – Interactive Analysis】: Reduce inconsistent results caused by frequent select-option switches on slow networks (restrict rapid clicks).

II. System

【Profile】: Allow channel users to set report logos, emails, phone numbers, and advanced-analysis report titles.

【Profile】: Refresh the AI mobile interface.

【Sample Projects】: Remove workflow members from sample projects.

【Parameter Templates】: Lower the minimum UMI threshold in the SeekGene Recommended template from 300 to 200.

V4.4.1.240613

Release Date: June 13, 2024

What's New:
I. Resource Overview

【My Data – Data Upload】: Calculate the number of samples in RDS files based on the Sample column and automatically deduct the corresponding upload quota; support datasets with up to 500,000 cells.

【Analysis Workflows – Basic Analysis】: Save gene-set filtering results to metadata.

【Analysis Workflows – Cell Annotation】: Sort gene-expression plots by cell name.

【Analysis Workflows – Plotting Tool】: Auto-adjust spatial image widths; add a filtering-factor option to bubble plots.

【Analysis Workflows – Interactive Analysis】: Support PNG and SVG downloads with added scale bars and legends.

【Analysis Workflows – Advanced Analysis】:

• GSVA: make <Grouping Factor> and <Group Comparison> mutually exclusive.
• CytoTRACE: require at least two cell types; rename split factor/object to filtering factor/object.
• monocle3, cellphonedb, infercnv: switch species from Latin to English and improve input-field validations.
• Fine-tune default parameters for monocle2.
• Optimize resource allocation for infercnv.
• CellChat: add a prompt noting that two steps are required to obtain results (see FAQ Q5).
• Refine error-handling logic for advanced analyses.

【Analysis Workflows – Result Overview】:

• Adjust the placement of auto-annotation results.
• Add chart-name columns for sequencing QC, library QC, and sample information.
• Improve annotations for ORA and GSEA enrichment results.

【Analysis Workflows – Auxiliary Information】: When downloading spatial RDS files, include HE and ssDNA PNG images.

II. System

【Online Consultation】: Introduce an AI-powered Q&A feature that responds first, with an option to escalate to human support; the AI mobile homepage now displays reminder text and will be added to the official account after redesign.

V4.3.1.240522

Release Date: May 22, 2024

What's New:
I. Resource Overview

【My Data – Data Upload】: Ensure RDS uploads contain both UMAP and t-SNE embeddings and that meta.data includes a Sample column; standardize UMAP naming.

【Analysis Workflows – Analysis Workflows】: Improve error messaging for workflows that fail to start.

【Analysis Workflows – Interactive Analysis】:

• Add image-position adjustments and undo/original-state actions.
• Allow reversing segmentation edits (treat adjustments and segmentation as image edits).
• Refresh the page styling.

【Analysis Workflows – Advanced Analysis】: Add a task ID column and enhance deletion logic.

• infercnv: require the <analysis cell type> and make it mutually exclusive with <reference cell type>.
• monocle2: require at least two cell types; make the filtering factor optional; add a downsample option and streamline analysis-type settings.
• monocle3: require <split factor> and record cell-type history.
• scenic: add a downsample option and adjust analysis-type settings.

【Analysis Workflows – Result Overview】: Prevent deletion failures caused by overly long cell names in Differential Enrichment results.

【My Databases – My Gene Sets】: Support searching/selecting species.

V4.2.1.240508

Release Date: May 8, 2024

What's New:
I. SeekSoulOnline Resource Overview

【Analysis Workflows – Data Upload】: Disallow NA values in RDS metadata; remove paths from matrix Barcode values.

【Analysis Workflows – Cell Annotation】: Improve caching for gene-set results.

【Analysis Workflows – Differential Enrichment】: Adjust headers imported into Result Overview based on enrichment-method parameters (GSEA/ORA).

【Analysis Workflows – Interactive Analysis】: Sync discrete-color palettes with Plotting Tool; add controls to adjust HE image color combinations.

【Analysis Workflows – Auxiliary Information】: In Tag Management, prevent editing of columns named Sample or starting with resolution.

【Analysis Workflows – Advanced Analysis】: Optimize cellphonedb, GSVA, and copyKAT workflows and improve monocle2 reruns.

【Analysis Workflows – Result Overview】: Add auto-annotation parameters to the statistics section; stack all plots; refine QC library tables.

II. System

【Link Login】: After clicking a workflow link, redirect users to the corresponding workflow post-login.

【User Management】: Add a third-party admin role to track external visits and registrations.

V4.2.1.240424

Release Date: April 24, 2024

What's New:
I. System

【Configuration Management】: Update parameter references and FAQs.

V4.1.2.240417

Release Date: April 17, 2024

What's New:
I. Resource Overview

【Analysis Workflows】: Improve workflow-numbering rules.

【My Data – Data Upload】: Enforce a 5 GB upload limit.

【Analysis Workflows – Plotting Tool】: Disable shared y-axes in violin plots by default.

【Analysis Workflows – Result Overview】: Enable downloads of historical reports and refine narrative descriptions.

【Analysis Workflows – Interactive Analysis】: Add HE background images and cropping tools.

II. System

【Online Consultation】: Improve linking between users and technical support.

【Workflow Management】: Enhance admin permissions for copying and sharing workflows.

V4.1.1.240320

Release Date: March 27, 2024

What's New:
I. Resource Overview

【My Data – Data Upload】: Add clarifications for standard-analysis results.

【Analysis Workflows – Interactive Analysis】: Introduce ssDNA image cropping and replacement.

【Analysis Workflows – Advanced Analysis】:

• Fine-tune parameters for monocle3, monocle2, scenic, cellphonedb, and DiffEnrich.
• Improve parameter autofill when rerunning analyses on historical results.
• Limit CellChat ligands/receptors to subsets of cell types.
• Add copyKAT, scMetabolism, GSVA, NicheNet, and scVelo modules.

【Analysis Workflows – Result Overview】: Add workflow links and new QC data.

II. System

【User Management】: Optimize the management interface.

【Online Consultation】: Improve unread-message notifications.

【Documentation】: Update guides for Advanced Analysis and Tag Management.

【Configuration Management】: Add the CellChat tutorial and clarify the difference between Feature Analysis and creating gene sets.

V4.0.20.240306

Release Date: March 6, 2024

What's New:
I. Resource Overview

【My Projects – Sample Projects】: Add spatial-analysis sample workflows.

【Analysis Workflows】: Introduce workflow IDs.

【Analysis Workflows – Cell Annotation】: Prevent entering gene names or special characters in label fields.

【Analysis Workflows – Basic Analysis】: Improve CCA error messages and the overlay mask shown during 【Complete】.

【Analysis Workflows – Cell Annotation】: Restrict cell names to letters, numbers, underscores, and spaces.

【Analysis Workflows – Plotting Tool】: Add expression-statistics tables to violin plots and refine legend placement across chart types.

【Analysis Workflows – Advanced Analysis】: Provide parameter documentation for BCR, TCR, CytoTRACE, and CellChat.

【Analysis Workflows – Auxiliary Information】: Add a Tag Management feature.

V4.0.18.240124

Release Date: January 24, 2024

What's New:
I. Resource Overview

【My Data – Data Upload】: Support features.tsv.gz files with a single column; enhance upload prompts and display permission quotas.

【Analysis Workflows】: Add workflow-member columns for per-workflow permissions.

【Analysis Workflows】: Standardize gene-set validation messages across Cell Annotation, Differential Enrichment, Plotting Tool, etc.

【Analysis Workflows – Plotting Tool】: Add a test-method toggle for violin plots; include statistics tables for dot plots (wrap labels >50 characters); update heatmap notes and annotations.

【Analysis Workflows – Subset Selection】: Allow sharing generated data among project members.

【Analysis Workflows – Differential Enrichment】: Auto-scale bubble-plot color ranges based on padj.

【Analysis Workflows – Advanced Analysis】: Add CytoTRACE and CellChat modules.

【Analysis Workflows – Result Overview】: Reposition the “Parameter Statistics” section.

V4.0.17.240111

Release Date: January 11, 2024

What's New:
I. Resource Overview

【Analysis Workflows – Basic Analysis】: Add a single-sample filtering statistics table and chain Basic Analysis → Cell Annotation → Plotting Tool → Differential Enrichment during initialization.

【Analysis Workflows – Advanced Analysis】: Allow scenic analyses to rerun on historical results and refine DiffEnrich.

【Analysis Workflows – Result Overview】: Improve typography and image sizing in aggregated results.

II. System

【Registration and Login】: Add SeekSoulOnline user policy and privacy notices to the login and registration pages.

V4.0.16.231227

Release Date: December 27, 2023

What's New:
I. Resource Overview

【Analysis Workflows】: Add editable contract IDs and names and provide parameter notes plus FAQs across all modules.

【Analysis Workflows – Basic Analysis】: Allow custom gene-set violin plots generated during filtering to be imported into Result Overview.

【Analysis Workflows – Cell Annotation】: Rename the marker-gene column from logFC to log2FC.

【Analysis Workflows – Plotting Tool】: Introduce custom auto-layout options.

【Analysis Workflows – Differential Enrichment】: Split bar chart summaries in Result Overview by comparison pair.

【Analysis Workflows – Interactive Analysis】: Add rectangle drawing for statistics and optimize processing performance.

【Analysis Workflows – Advanced Analysis】: Add combined TCR + BCR analysis.

【Analysis Workflows – Result Overview】: Allow same-level headings to be rearranged.

【Auxiliary Information】: Move the Samples table into Result Overview.

V4.0.15.231213

Release Date: December 13, 2023

What's New:
I. Resource Overview

【My Projects – Sample Projects】: Update advanced-analysis reports to the latest version.

【Analysis Workflows – Basic Analysis】: Improve CCA integration error messaging and add parameter notes plus FAQ links.

【Analysis Workflows – Cell Annotation】: Adjust prompts so workflows with only one cell type cannot proceed or be saved.

【Analysis Workflows – Differential Enrichment】: Align heatmap ordering with comparison sequences and lowercase term names in enrichment outputs.

【Analysis Workflows – Interactive Analysis】: Add “select all factors,” fullscreen display, and convert the metadata tagging input to a searchable dropdown.

【Analysis Workflows – Advanced Analysis】: Enable scenic to analyze single cell types and update report file naming.

V4.0.12.231130

Release Date: November 30, 2023

What's New:
I. Resource Overview

【Parameter Templates】: Update SeekGene Recommended parameters.

【My Projects】: Sort projects by last update time and add onboarding guidance from Resource Overview to workflow creation.

【My Data – Data Upload】: Introduce sharing so uploaded samples can be shared with other accounts.

【Analysis Workflows】: Display species names in Latin (English).

【Analysis Workflows – Basic Analysis】: Refine sample-selection order and speed up page loading.

【Analysis Workflows – Cell Annotation】: Improve resolution-deletion logic.

【Analysis Workflows – Plotting Tool】: Add Arial to the font list.

【Analysis Workflows – Feature Analysis】: Dim the screen when viewing summaries for clearer focus.

【Analysis Workflows – Differential Enrichment】: Add a search box beneath comparison pairs.

【Analysis Workflows – Interactive Analysis】: Introduce an interactive module for combining transcriptomics with the SeekSpace spatial product.

【Analysis Workflows – Advanced Analysis】: Add cluster-level Differential Enrichment (Diffenrich).

【Analysis Workflows – Result Overview】: Reorder Differential Enrichment outputs for clarity.

II. System

【Login】: Add password-recovery functionality and restrict simultaneous logins to one device per account.

【User Management】: Improve expiration and data-release email templates.

V4.0.12.231101

Release Date: November 15, 2023

What's New:
I. Resource Overview

【Parameter Templates】: Add GO, KEGG, and REACTOME databases to the SeekGene Recommended template; keep gene-set filtering empty by default.

【Analysis Workflows】: Rename import buttons to “Aggregate,” convert download icons to text buttons, and keep workflow status refreshed in real time.

【My Data – Data Upload】: Enhance matrix uploads to support multi-select.

【Analysis Workflows – Basic Analysis】: Improve the progress bar and add estimated time hints.

【Analysis Workflows – Cell Annotation】: Allow top-gene dialogs to create gene sets and include project/workflow metadata in downloaded files.

【Analysis Workflows – Plotting Tool】: Use the Add Tag feature to mark cells by expression levels.

【Analysis Workflows – Feature Analysis】: Permit importing images into Result Overview.

【Analysis Workflows – Result Overview】: Include project, group, and comparison details in downloaded enrichment tables and refine report wording/structure.

II. System

【Online Consultation】: Optimize consultation flow.

【Configuration Management】: Add a configuration center for parameter and result explanations.

V4.0.11.231018

Release Date: October 18, 2023

What's New:
I. Resource Overview

【My Databases】: Link databases to gene sets.

【Analysis Workflows】: Allow workflow names and descriptions to be edited at any time.

【Analysis Workflows – Basic Analysis】: Auto-match species data during workflows; leave fields blank and prompt users if no match is found.

【Analysis Workflows – Cell Annotation】: Add zoom controls for Cell Annotation and Differential Enrichment pages.

【Analysis Workflows – Plotting Tool】: Support reordering group and split factors and provide palette adjustments.

【Analysis Workflows – Differential Enrichment】: Allow custom bubble plots.

V4.0.10.230927

Release Date: September 27, 2023

What's New:
I. Resource Overview

【Analysis Workflows – Plotting Tool】: Add font customization and a “clear features” control.

【Analysis Workflows – Auxiliary Information】: Deliver downloads through temporary links.

II. System

【Online Consultation】: Launch live consultation services.

【Permissions】: Add per-workflow permission management.

V4.0.9.230920

Release Date: September 20, 2023

What's New:
I. Resource Overview

【My Projects】: Improve account matching for shared projects.

【My Databases】: Default to original names when adding databases or gene sets (with edit support).

【Analysis Workflows】: Refine species configuration.

【Analysis Workflows – Basic Analysis】: Enhance completion logic and fix the bug where applying filters failed to reset results.

【Analysis Workflows – Cell Annotation】: Improve save logic, enable table downloads, add import-to-Result Overview, and provide category tags in reference sets.

【Analysis Workflows – Differential Enrichment】: Add overlays when summarizing differential results.

【Analysis Workflows – Subset Selection】: Auto-select the relevant data when launching a new subset workflow.

【Analysis Workflows – Advanced Analysis】: Enhance runtime environments and adjust infercnv parameters.

【Analysis Workflows – Auxiliary Information】: Streamline data downloads.

【Analysis Workflows – Result Overview】: Make basic-analysis images clickable to jump to the originating module.

V4.0.8.230906

Release Date: September 6, 2023

What's New:
I. Resource Overview

【Parameter Templates】: Change the continuous-color palette to gray-to-blue.

【Analysis Workflows】: Add workflow duplication.

【My Projects – Sample Projects】: Provide a transcriptomics sample project.

【Analysis Workflows – Result Overview】: Replace the Original Data Exploration module with Result Overview and streamline the report structure.

【Analysis Workflows – Differential Enrichment】: Allow creating new comparison groups when adding comparison schemes and support one-click imports of comparison results.

【Analysis Workflows – Auxiliary Information】: Restrict data downloads (technical support and customers cannot download raw files).

II. System

【Login】: Adjust permissions for registered users.

【Layout】: Add customizable title-bar themes and refresh UI styling.

V4.0.7.230823

Release Date: August 23, 2023

What's New:
I. Resource Overview

【My Databases】: Refine species selection for databases and gene sets.

【Analysis Workflows – Cell Annotation】: Improve auto-annotation logic, sync FeaturePlot and dimensionality-reduction methods, and add gene-table downloads.

【Analysis Workflows – Differential Enrichment】: Improve alignment between differential figures and tables and add enrichment-table downloads.

【Analysis Workflows – Plotting Tool】: Introduce a top-level menu.

II. System

【Login】: Enable self-service registration, adjust default permissions, and require phone verification.

【User Management】: Update displayed account details and refine creation/expiration workflows.

【Layout】: Refresh the UI.

V4.0.6.230809

Release Date: August 10, 2023

What's New:
I. Resource Overview

【Analysis Workflows – Advanced Analysis】: Add the monocle2 module.

【Analysis Workflows – Differential Enrichment】: Support between-group Differential Enrichment analyses with combined Cell Annotation/Differential Enrichment reports.

【Analysis Workflows – Basic Analysis】: Provide automated pipelines for “Basic Analysis + Cell Annotation” and “Basic Analysis + Cell Annotation + Differential Enrichment,” and auto-refresh progress.

【Analysis Workflows – Plotting Tool】: Add description fields and collapse gene lists by default.

II. System

【Parameter Templates】: Add parameters for differential and enrichment analyses plus custom colors.

【Layout】: Refresh the overall theme.

【Resource Settings】: Optimize resources to support datasets with ~200k cells.

V4.0.5.230703

Release Date: July 3, 2023

What's New:
I. Resource Overview

【My Data – Data Upload】: Support RDS files generated from Auxiliary Information downloads.

【Analysis Workflows – Cell Annotation】: Update and enhance the module.

【Analysis Workflows – Basic Analysis】: Add one-click analysis and polish documentation.

【Analysis Workflows – Plotting Tool】: Introduce significance tests for violin plots and allow creating gene sets directly from the features parameter.

【Analysis Workflows – Feature Analysis】: Support adding custom feature sets.

【Analysis Workflows – Differential Enrichment】: Fix absolute-value selection issues in enrichment analysis.

【Analysis Workflows – Advanced Analysis】: Optimize resource allocation and use all cells for infercnv.

V4.0.4.230609

Release Date: June 9, 2023

What's New:
I. Resource Overview

【Resource Overview】: Improve My Databases, My Gene Sets, Parameter Templates, and Help documentation.

【My Data】: Display original matrices, samples, subsets, and standard-analysis results.

【Analysis Workflows – Basic Analysis】: Refine layout/logic to allow repeating steps before completion; permit skipping integration/clustering after initializing standard RDS files; source parameters and animation colors from selected templates.

【Analysis Workflows – Plotting Tool】: Improve grouping and sorting, allow drag-and-drop for features, support single/multi-select group factors, refine group/split displays, optimize plotting data, and add pie charts.

Release Date: May 11, 2023

What's New:
I. Resource Overview

【Resource Overview】: Add My Databases, My Gene Sets, Parameter Templates, and Help modules.

【Analysis Workflows – Plotting Tool】: Rename the Data Exploration module to Plotting Tool.

II. System

【Login】: Switch the login URL to use the domain name.

V4.0.1.230420

Release Date: April 20, 2023

What's New:
I. Resource Overview (formerly Analysis Projects)

【Analysis Projects】: Rename to Resource Overview, restructure the page, add “My Projects” and “My Data” lists, and update the 【Create Project】 and 【Quick Workflow】 buttons alongside data-upload logic.

【My Projects】: Introduce project sharing and refine project numbering rules.

【Analysis Workflows】: Refresh the workflow list UI and add a “Close Workflow” option.

【Analysis Workflows – Data Exploration】: Show download-in-progress indicators.

【Analysis Workflows – Differential Enrichment】: Show download-in-progress indicators.

II. System

【Lists】: Beautify table layouts and support search/sort actions.

V4.0.0.230406

Release Date: April 7, 2023

What's New:
I. Resource Overview

【Analysis Projects – Data Exploration】: Add grouped plotting, allow reordering images within/among groups, toggle cell-count legends, toggle labels, and adjust gradient ranges.

【Analysis Projects – Differential Enrichment】: Improve Y-axis labeling in bubble charts.

II. System

【Login】: Limit failed password attempts to five; additional attempts require a 30-minute wait.

【Profile】: Add profile display and edit features.

【Layout】: Refresh the overall site structure.

V3.0.0.230320

Release Date: March 20, 2023

What's New:
I. Resource Overview

【Analysis Workflows】: Enable downloading cloud-platform report tables.

【My Data – Data Upload】: Speed up uploads.

【Analysis Workflows – Plotting Tool】: Add heatmap generation.

【Analysis Workflows – Feature Analysis】: Support multi-dataset analyses.