Git Product home page Git Product logo

genexvis's Introduction

Javascript Vue.js NW.js Release

GenExVis (Gene Expression Visualizer)

Contents

Description

The gene expression visualizer (GenExVis) is an easy-to-use application for exploring and visualizing differential gene expression data created with DESeq2. It can display various charts and tables from simple count tables and DESeq2 result files without the necessity of uploading any data or installing any packages.

Features

GenExVis was developed for a fast and straightforward first look at transcriptomic data analyzed with DESeq2. After importing a count table (e.g., from featureCounts) and the results of a DESeq2 comparison (see Using GenExVis), you can explore your data in various charts, a ranking by different criteria, or an overview table with filter options. GenExVis also supports the creation of gene subsets for specified charts containing only a selected number of genes. features_collage

Usage

Installation

There is nothing really to install. Just download GenExVis for your OS here and extract the downloaded archive. On Windows, start GenExVis per double-click on 'start_genexvis.exe' and on Linux per execution of 'start_genexvis'.

Using GenExVis

After starting GenExVis, you need to define your experimental conditions and import your count table and DESeq2 comparison files. import_collage

Experimental conditions (top left image)

For a correct assignment of conditions to gene counts and DESeq2 data, you have to register the experimental conditions first. Therefore, you can either import them by hand via the text field or by text file (one condition per line). GenExVis will try its best to auto-assign your count table columns and DESeq2 comparisons to these conditions.

Count Table (top right image)

Currently, GenExVis supports column-based tab-separated count tables with genes/features as rows and experiments/sequencing runs as columns. After choosing a file, you will get an overview of all columns in this file, and GenExVis will try to detect the gene name column (--Feature name--) and auto-assign a condition to experiment columns. For this to work, GenExVis searches the column header for the registered conditions. If there are any columns in your count table which you don't want to import, just select --Ignore--. Besides all those entries corresponding to your count table, you also have to choose the normalization method of these counts. At the moment, this is pure metadata and is used by GenExVis to give the user option to work with two count tables in parallel (raw and normalized).

DESeq2 comparison (top right image)

A DESeq2 comparison file (see example below) is a tab-separated text file containing the DESeq2 results of one comparison (Condition A vs. Condition B). These files can be automatically genereated in DESEq2 with the following commands:

res <- results(dds, contrast=c("condition","treated","untreated"))
write.table(res, file = 'treated_vs_untreated.tsv', sep = "\t", row.names = TRUE, col.names = NA)

If your filename is in the format ..._<condA_vs_<condB>.tsv (e.g., deseq2_WT_vs_Mut.tsv), GenExVis can automatically assign the correct conditions for this comparison.

Example:

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
WP_001386572.1	45.5357893182288	-0.05022152209245	0.306102011607642	-0.164067925684931	0.869677671214074	0.956740544473097
WP_000526115.1	20.3776406578987	0.408701212605221	0.386501810430336	1.05743673529024	0.290312313469477	0.575376359024185
WP_001264710.1	1029.58523755302	0.321829338807359	0.147298326663496	2.18488115986939	0.028897561237329	0.118153993536635
WP_000241663.1	297.019706092551	0.202059896894583	0.170039822767809	1.18830926547423	0.234711588669142	0.509999045693777
WP_000781042.1	460.507885104470	-0.044135348864798	0.164979488062347	-0.267520219532493	0.789068648359211	0.922804907369967
WP_001102391.1	1.21713032581618	-1.10175048525465	1.50339386731804	-0.732842210684352	0.463654673013483	NA

Citation

Blumenkamp, P., Pfister, M., Diedrich, S., Brinkrolf, K., Jaenicke, S., Goesmann, A. - Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data. BMC Bioinformatics 25, 138 (2024). https://doi.org/10.1186/s12859-024-05761-2

FAQ

  1. Contact and support: [email protected]
  2. Issues: Bugs and issues can be filed here

genexvis's People

Contributors

miriammueller avatar pblumenkamp avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar

genexvis's Issues

Deseq2 overview 2 to Developement - [merged]

In GitLab by @jwinter on Jun 20, 2018, 13:23

Merges deseq2_overview_2 -> development

  • Extended the parsers "ignore-situations" (2 fields, 1 match AND 1 field, 2 matches)
  • Removed "TEST" at Volcano Plot
  • Added several "scoped" in "<style>".

Ready to merge.

DESeq2 Overview for large datasets

  • from 2,000,000 cells upwards the ag-grid table should get replaced by a more efficient (but less features) table (bootstrap table?) (@pblumenk)
  • by default, lfcSE, p-value, and stat should be hidden (with an option to show them)
  • it should also be possible to hide a comparison completely in the ag-grid table
  • there should be an option to download the table (tsv, csv, xlsx) (@pblumenk)
  • download the subset (tsv, csv, xlsx) (@pblumenk)

npm run dev: TypeError: Cannot read property 'properties' of undefined.... (package.json issue with webpack and webpack-cli)

In GitLab by @mmueller on Apr 15, 2019, 09:26

  • cloned git repository
  • ran npm install
  • npm run dev resulted in error "TypeError: Cannot read property 'properties' of undefined "
    fixed with changing webpack and webpack-cli to the following in package.json
    (plotly/dash-component-boilerplate#12)

"webpack": "^4.20.2"

"webpack-cli": "^3.1.1"


then ran npm install --save webpack-cli

-> other versions of webpack and webpack-cli not necessary, but the npm install --save webpack-cli seems to be.

Deseq2 overview 2 - [merged]

In GitLab by @jwinter on Aug 5, 2018, 11:10

Merges deseq2_overview_2 -> development

DESeq2_overview_2 müsste fertig sein. Zu beachten wäre, dass du an anderer Stelle schon die Farben der Balken geändert hast (DESeq2_Overview, Tabelle, Log2FoldChange).

Exchange volcano plot series for highcharts zones [REPLACEMENT ISSUE]

The original issue

Id: 13
Title: Exchange volcano plot series for highcharts zones

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

counts vs. counts scatter plot [REPLACEMENT ISSUE]

The original issue

Id: 26
Title: counts vs. counts scatter plot

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

Replace Set by Array for normalizationMethods in Dge [REPLACEMENT ISSUE]

The original issue

Id: 18
Title: Replace Set by Array for normalizationMethods in Dge

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

Histograms for count data [REPLACEMENT ISSUE]

The original issue

Id: 17
Title: Histograms for count data

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

check conditions to be valid in file uploader [REPLACEMENT ISSUE]

The original issue

Id: 2
Title: check conditions to be valid in file uploader

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

gene_0 missing (upload function)

In GitLab by @mmueller on Apr 15, 2019, 13:16

  • upload of deseq2_results (e.g. _t0_Vs._t1_large.csv) results in gene_0 missing in store

  • .csv has 1Mio entries (starting with gene_0)

  • DGE store says: 999.999 genes, starting with gene_1

log2 fold change histogram [REPLACEMENT ISSUE]

The original issue

Id: 22
Title: log2 fold change histogram

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

Warnings when opening DESeq2 overview

In GitLab by @[email protected] on Jul 17, 2018, 13:33

A lot of warnings appear on the web console if "Deseq2 overview" is opened with the test data.

  • ag-grid: invalid gridOptions property 'ob' did you mean any of these:
    groupSuppressBlankHeader,slaveGrids,rowData,columnDefs,excelStyles,pinnedTopRowData,pinnedBottomRowData,components

  • gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid gridOptions properties please check: https://www.ag-grid.com/javascript-grid-properties/

  • gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

  • gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
    GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132

  • gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

  • gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
    GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132

  • gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

  • gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
    GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132

  • gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent

  • gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/

Import of multiple count tables [REPLACEMENT ISSUE]

The original issue

Id: 27
Title: Import of multiple count tables

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

p-Value histogram [REPLACEMENT ISSUE]

The original issue

Id: 21
Title: p-Value histogram

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

DESeq2 IDs and GFF3 IDs

In GitLab by @mmueller on Aug 8, 2019, 10:56

Metadata and DESeq2 data are merged based on full feature IDs. If the IDs do not match fully, import for a gff will be blocked. Might lead to problems, if the user changed IDs during data processing (featureCounts, gff).

Improvements for "Current subset" box

In GitLab by @[email protected] on Mar 28, 2019, 12:53

  • True/false next to "Current subset:" can be deleted
  • A small gap between the genes box and the Clear button
  • +/- should be inverted (swap + with - and vice versa)
  • bigger margin for the inner box (the one containing all subset genes). The gap between the gene button and the outer box should be increased

current_subset

Integration of raw data [REPLACEMENT ISSUE]

The original issue

Id: 6
Title: Integration of raw data

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

reset dge object

In GitLab by @[email protected] on Mar 13, 2018, 12:44

There should be a way to reset/empty the dge object. This includes frontend work and adding new actions and mutations to the vuex store.

Does not update subset if subset is currently selected [REPLACEMENT ISSUE]

The original issue

Id: 19
Title: Does not update subset if subset is currently selected

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.