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GitHub / zqfang/GSEApy issues and pull requests

#309 - bug report: Offline enrichr cannot set background to int

Issue - State: closed - Opened by solo7773 5 months ago - 1 comment

#308 - bug report: gene names misordered

Issue - State: open - Opened by alexfields 5 months ago

#307 - Installation of 1.1.7 version fail without rust compiler

Issue - State: closed - Opened by thomasgaudelet 6 months ago - 3 comments

#306 - AttributeError: 'numpy.int64' object has no attribute 'upper'

Issue - State: closed - Opened by Nazim0001 6 months ago - 6 comments

#305 - Remove gsea_gmt_parser from docs

Issue - State: closed - Opened by pdegen 7 months ago - 1 comment

#304 - Different Results Between Versions?

Issue - State: closed - Opened by TomYoung03 7 months ago - 2 comments

#303 - Failing with 1.1.5 - empty gene list not excluded

Issue - State: closed - Opened by enryH 7 months ago - 6 comments

#301 - Only check_uppercase for string genes

Pull Request - State: closed - Opened by brenshanny 7 months ago

#301 - Only check_uppercase for string genes

Pull Request - State: closed - Opened by brenshanny 7 months ago

#300 - JSONDecodeError when using a small background list

Issue - State: open - Opened by wongkarenhy-hex 7 months ago - 15 comments

#299 - Example single cell data

Issue - State: closed - Opened by Capiques 7 months ago - 3 comments

#298 - mismatched tag when using biomart to get mouse to human gene mappings

Issue - State: closed - Opened by dmalzl 8 months ago - 1 comment

#297 - Patch-1

Pull Request - State: closed - Opened by wrb2012 8 months ago - 2 comments

#297 - Patch-1

Pull Request - State: closed - Opened by wrb2012 8 months ago - 1 comment

#296 - feature request: LLM generated gene sets

Issue - State: open - Opened by zia1138 8 months ago

#294 - GSVA analysis

Issue - State: open - Opened by free-sky9527 9 months ago

#292 - Handling Isolated Nodes in Network Visualization for 'gseapy_example'

Issue - State: closed - Opened by xiiyao 9 months ago - 2 comments

#287 - no result after ssgsea

Issue - State: closed - Opened by Nazim0001 10 months ago

#285 - [Feature request] Overlay multiple dotplots on the same ax

Issue - State: closed - Opened by Puumanamana 10 months ago - 1 comment

#281 - Update plot.py

Pull Request - State: closed - Opened by byemaxx 12 months ago

#281 - Update plot.py

Pull Request - State: closed - Opened by byemaxx 12 months ago

#279 - dotplot AttributeError

Issue - State: closed - Opened by ymy948 12 months ago - 3 comments

#278 - fix: throw error for empty gene lists in enrich

Pull Request - State: closed - Opened by quasi-deus 12 months ago

#278 - fix: throw error for empty gene lists in enrich

Pull Request - State: closed - Opened by quasi-deus 12 months ago - 1 comment

#277 - high memory consumption when using gsva

Issue - State: open - Opened by dmalzl 12 months ago

#276 - gene sets score and gsva

Issue - State: open - Opened by wangjiawen2013 12 months ago

#274 - dotplot legend label error

Issue - State: closed - Opened by loriglenwinkel about 1 year ago - 1 comment

#273 - Enrichment_map Top_term Param Inconsistencies

Issue - State: open - Opened by Tripfantasy about 1 year ago

#272 - New implementation of GSEA and gseaplot()

Issue - State: open - Opened by DavideBiondi about 1 year ago

#271 - Running gp.enrich() with custom gene_sets throwing error.

Issue - State: closed - Opened by asif7adil about 1 year ago - 4 comments

#270 - Missing one input gene into Prerank module

Issue - State: closed - Opened by wgsim about 1 year ago - 1 comment

#269 - The difference between input gene symbol name and geneID

Issue - State: open - Opened by lxy04 about 1 year ago

#268 - gseaplot how to do to reset the label/NES etc. font size and set the FDR display

Issue - State: closed - Opened by lxy04 over 1 year ago - 1 comment

#267 - Prerank function not reading gmt files correctly

Issue - State: closed - Opened by avdl25 over 1 year ago - 2 comments

#265 - Missing wheels for Python 3.12 on PyPI

Issue - State: closed - Opened by ecederstrand over 1 year ago - 2 comments

#261 - is it able to change the order of cls item

Issue - State: closed - Opened by hfl112 over 1 year ago - 2 comments

#260 - Only last one used when params `gene_sets` is given as list

Issue - State: closed - Opened by zhouzhendiao over 1 year ago - 2 comments

#259 - Could not return matplotlib.Axes in python script

Issue - State: open - Opened by AfterDream over 1 year ago - 3 comments

#258 - 'DataFrame' object has no attribute 'append'

Issue - State: open - Opened by rubickkkkk over 1 year ago - 3 comments

#256 - Using a count matrix with NA values for GSEApy

Issue - State: open - Opened by LeilyR over 1 year ago

#255 - key error

Issue - State: closed - Opened by anke-king over 1 year ago - 5 comments

#252 - Prerank fails with list of gene sets

Issue - State: open - Opened by CDSchuster over 1 year ago

#251 - Error with prerank, after updating to newest version of GSEApy

Issue - State: closed - Opened by jasiozaucha over 1 year ago - 1 comment

#249 - align gene hits track in TracePlot (fixes zqfang/GSEApy#248)

Pull Request - State: closed - Opened by 136s over 1 year ago

#249 - align gene hits track in TracePlot (fixes zqfang/GSEApy#248)

Pull Request - State: open - Opened by 136s over 1 year ago

#248 - Incorrect position of hit in gseaplot2 like #222

Issue - State: open - Opened by 136s over 1 year ago

#247 - Error running prerank

Issue - State: closed - Opened by spatts14 over 1 year ago - 2 comments

#246 - cannot import GSEApy

Issue - State: closed - Opened by spatts14 over 1 year ago

#245 - Error sending data

Issue - State: open - Opened by mousepixels over 1 year ago

#244 - if Item less than 15, dotplot can't work for GSEA result.

Issue - State: closed - Opened by li1311139481 over 1 year ago - 11 comments

#243 - issues with enrichr

Issue - State: closed - Opened by SaBay89 over 1 year ago - 2 comments

#241 - Mssing "Term" value when using enrich function with custom gene_sets

Issue - State: closed - Opened by ttbond over 1 year ago - 1 comment

#240 - Fixed to run prerank without error with rnk (type(pd.Series.name) == str)

Pull Request - State: closed - Opened by 136s over 1 year ago

#239 - Cannot execute Prerank with pandas.Series which type of name is str as rank

Issue - State: closed - Opened by 136s over 1 year ago - 1 comment

#238 - Corrected odds ratio formula, #237

Pull Request - State: closed - Opened by 136s over 1 year ago

#237 - Odds ratios differ between enrichr and `gseapy.enrich()`

Issue - State: closed - Opened by 136s over 1 year ago - 3 comments

#236 - Handling genes with zero expression when using gp.gsea

Issue - State: open - Opened by looppy95 almost 2 years ago - 1 comment

#235 - Error getting the Enrichr libraries

Issue - State: open - Opened by talponer almost 2 years ago - 7 comments

#234 - TypeError: argument 'genes': 'int' object cannot be converted to 'PyString'

Issue - State: closed - Opened by Ci-TJ almost 2 years ago - 2 comments

#233 - Exited with code=null when apply gseapy for a big .gmt file

Issue - State: closed - Opened by Sunmile almost 2 years ago - 2 comments

#232 - NES values are set to 0

Issue - State: closed - Opened by alegiac95 almost 2 years ago - 2 comments

#231 - A question about AttributeError

Issue - State: closed - Opened by chulexuexibiedebushihewo almost 2 years ago

#230 - column name 'Term' in the second line

Issue - State: closed - Opened by SherylShaw almost 2 years ago - 1 comment

#229 - How to get lead genes from ssGSEA object

Issue - State: open - Opened by Num0Programmer almost 2 years ago - 1 comment

#228 - Interpret GSEA plot

Issue - State: open - Opened by Cher-HAN almost 2 years ago

#227 - Update gseapy_tutorial.rst

Pull Request - State: closed - Opened by abhi-glitchhg almost 2 years ago

#226 - Suggesting integration of GSVA

Issue - State: closed - Opened by ftamiro almost 2 years ago - 2 comments

#224 - Improvement request for barplot

Issue - State: closed - Opened by princessEmilyy almost 2 years ago - 1 comment

#223 - Can we get correct p-values and FDRs in ssgsea now?

Issue - State: open - Opened by Peevin almost 2 years ago - 1 comment

#222 - The bars in the center panel are misaligned.

Issue - State: closed - Opened by searchlie about 2 years ago - 2 comments

#220 - Traceplot does not save figure

Issue - State: closed - Opened by jfinkle1016 about 2 years ago

#218 - KeyError: "'de novo' posttranslational protein folding (GO:0051084)"

Issue - State: closed - Opened by nargesr about 2 years ago - 4 comments

#214 - No module named 'gseapy.gse'

Issue - State: open - Opened by ShriHarshaAdapalaThirumala about 2 years ago - 8 comments
Labels: FAQ

#213 - Can not import a package after update

Issue - State: closed - Opened by azbukinanadezda about 2 years ago - 5 comments

#212 - Dotplot annotations

Issue - State: closed - Opened by BelanaZ about 2 years ago - 1 comment

#209 - Getting precise FDR values and plotting if values are 0

Issue - State: open - Opened by ThomasThaewel about 2 years ago - 1 comment
Labels: FAQ

#208 - FDR q-val does not preserve ordering of nominal p-values

Issue - State: closed - Opened by joshscurll over 2 years ago - 2 comments

#207 - Tests in src/stats.rs reference invalid fields

Issue - State: closed - Opened by rekado over 2 years ago - 1 comment

#201 - Zeros in GSEA result

Issue - State: closed - Opened by hfl112 over 2 years ago - 1 comment

#200 - Matplotlib support failed

Issue - State: closed - Opened by Skychou-source over 2 years ago - 2 comments

#197 - two gene sets GSEA, DGSEA module

Issue - State: open - Opened by abearab over 2 years ago - 2 comments

#196 - Can I use GSEApy for gene enrichment analysis of non-model organisms?

Issue - State: closed - Opened by Skychou-source over 2 years ago - 7 comments

#195 - Dotplot ignoring arguments

Issue - State: closed - Opened by NicolasSompairac over 2 years ago - 4 comments

#194 - ssGSEA ignores parameters in 1.0.4

Issue - State: closed - Opened by verheytb over 2 years ago - 3 comments

#193 - PanicException: called Option::unwrap() on a None value

Issue - State: open - Opened by nroak over 2 years ago - 13 comments