Ecosyste.ms: Issues

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GitHub / zqfang/GSEApy issues and pull requests

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

Issue - State: open - Opened by lxy04 20 days ago - 1 comment

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

Issue - State: open - Opened by lxy04 about 1 month ago - 1 comment

#267 - Prerank function not reading gmt files correctly

Issue - State: closed - Opened by avdl25 about 2 months ago - 2 comments

#265 - Missing wheels for Python 3.12 on PyPI

Issue - State: closed - Opened by ecederstrand about 2 months ago - 2 comments

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

Issue - State: closed - Opened by hfl112 3 months ago - 2 comments

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

Issue - State: closed - Opened by zhouzhendiao 3 months ago - 2 comments

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

Issue - State: open - Opened by AfterDream 3 months ago - 1 comment

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

Issue - State: open - Opened by rubickkkkk 3 months ago - 2 comments

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

Issue - State: open - Opened by LeilyR 3 months ago - 1 comment

#255 - key error

Issue - State: open - Opened by anke-king 4 months ago - 5 comments

#253 - `log2_ratio_of_classes` required number of samples in the group >=3

Issue - State: closed - Opened by Liripo 4 months ago - 6 comments

#252 - Prerank fails with list of gene sets

Issue - State: open - Opened by CDSchuster 4 months ago - 1 comment

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

Issue - State: closed - Opened by jasiozaucha 4 months ago - 1 comment

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

Pull Request - State: closed - Opened by 136s 4 months ago

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

Issue - State: closed - Opened by 136s 4 months ago - 5 comments

#247 - Error running prerank

Issue - State: closed - Opened by spatts14 4 months ago - 2 comments

#246 - cannot import GSEApy

Issue - State: closed - Opened by spatts14 4 months ago

#245 - Error sending data

Issue - State: open - Opened by mousepixels 5 months ago - 2 comments

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

Issue - State: closed - Opened by li1311139481 5 months ago - 11 comments

#243 - issues with enrichr

Issue - State: open - Opened by SaBay89 5 months ago - 2 comments

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

Issue - State: closed - Opened by ttbond 6 months ago - 1 comment

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

Issue - State: closed - Opened by 136s 6 months ago - 1 comment

#238 - Corrected odds ratio formula, #237

Pull Request - State: closed - Opened by 136s 7 months ago

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

Issue - State: closed - Opened by 136s 7 months ago - 3 comments

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

Issue - State: open - Opened by looppy95 7 months ago - 1 comment

#235 - Error getting the Enrichr libraries

Issue - State: open - Opened by talponer 7 months ago - 7 comments

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

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

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

Issue - State: closed - Opened by Sunmile 8 months ago - 2 comments

#232 - NES values are set to 0

Issue - State: closed - Opened by alegiac95 8 months ago - 2 comments

#231 - A question about AttributeError

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

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

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

#229 - How to get lead genes from ssGSEA object

Issue - State: open - Opened by Num0Programmer 8 months ago - 1 comment

#228 - Interpret GSEA plot

Issue - State: open - Opened by Cher-HAN 9 months ago

#227 - Update gseapy_tutorial.rst

Pull Request - State: closed - Opened by abhi-glitchhg 9 months ago

#226 - Suggesting integration of GSVA

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

#224 - Improvement request for barplot

Issue - State: closed - Opened by princessEmilyy 9 months ago - 1 comment

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

Issue - State: open - Opened by Peevin 9 months ago - 1 comment

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

Issue - State: closed - Opened by searchlie 10 months ago - 2 comments

#221 - Pass filename to traceplot to enable saving

Pull Request - State: closed - Opened by jfinkle1016 11 months ago

#220 - Traceplot does not save figure

Issue - State: closed - Opened by jfinkle1016 11 months ago

#219 - ORA (enrichr) by offline doesn't work with Entrez Gene IDs.

Issue - State: closed - Opened by 136s 11 months ago - 2 comments

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

Issue - State: closed - Opened by nargesr 11 months ago - 4 comments

#214 - No module named 'gseapy.gse'

Issue - State: open - Opened by ShriHarshaAdapalaThirumala 12 months ago - 6 comments
Labels: FAQ

#213 - Can not import a package after update

Issue - State: closed - Opened by azbukinanadezda 12 months ago - 5 comments

#212 - Dotplot annotations

Issue - State: closed - Opened by BelanaZ 12 months ago - 1 comment

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

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

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

Issue - State: closed - Opened by joshscurll about 1 year ago - 2 comments

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

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

#204 - How to preserve mouse specific genes when downloading it from get_library()

Issue - State: closed - Opened by Smilenone about 1 year ago - 3 comments

#201 - Zeros in GSEA result

Issue - State: closed - Opened by hfl112 about 1 year ago - 1 comment

#200 - Matplotlib support failed

Issue - State: closed - Opened by Skychou-source about 1 year ago - 2 comments

#197 - two gene sets GSEA, DGSEA module

Issue - State: open - Opened by abearab about 1 year ago - 2 comments

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

Issue - State: closed - Opened by Skychou-source about 1 year ago - 7 comments

#195 - Dotplot ignoring arguments

Issue - State: closed - Opened by NicolasSompairac over 1 year ago - 4 comments

#194 - ssGSEA ignores parameters in 1.0.4

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

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

Issue - State: open - Opened by nroak over 1 year ago - 6 comments

#191 - New anaconda package install broken

Issue - State: closed - Opened by nwieder over 1 year ago - 7 comments

#190 - Genes in Lead_genes and heatmap are wrong when using gene_set permutation

Issue - State: closed - Opened by kyungtaekLIM over 1 year ago - 6 comments
Labels: bug, fixed, critical

#189 - Dotplot param type is incorrect

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

#186 - Broken link in SingleSampleGSEA normalization documentation

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

#185 - Specifying GO term levels OR term size with EnrichR

Issue - State: open - Opened by sruthi-hub over 1 year ago
Labels: enhancement, New Feature

#184 - Request demo data

Issue - State: closed - Opened by partrita over 1 year ago - 2 comments
Labels: done

#183 - ImportError: cannot import name 'enrichment_map' from 'gseapy.plot'

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

#182 - `Biomart().query` returns request status together with results

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

#181 - Suggestion: More informative "Gene_set" information in custom Enrichr run

Issue - State: closed - Opened by dnjst over 1 year ago - 2 comments
Labels: enhancement

#180 - Sporadic permission error on Windows when running preranked analysis

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

#179 - unrecognized arguments: -d pathway_enrichment

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

#178 - gseapy.gsea() is it bug?

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

#175 - error with dotplot()

Issue - State: closed - Opened by nargesr over 1 year ago - 7 comments

#174 - Data storage is unstable

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

#171 - unable to get ax when calling barplot()

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

#170 - pyo3_runtime.PanicException: called `Option::unwrap()` on a `None`

Issue - State: closed - Opened by kanekalla over 1 year ago - 6 comments

#169 - Missing plots after running GSEA

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

#168 - /lib64/libc.so.6: version `GLIBC_2.25' not found

Issue - State: closed - Opened by HelloWorldLTY over 1 year ago - 7 comments

#166 - install error on Google Colab

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

#165 - KeyError: 'Adjusted P-value' in dotplot

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

#163 - RUST compiler?

Issue - State: open - Opened by michaelmather15 almost 2 years ago - 7 comments
Labels: question, fixed, FAQ

#162 - Why is it possible for a p=0 term to have q=1?

Issue - State: closed - Opened by searchlie almost 2 years ago - 10 comments
Labels: bug, fixed, critical

#161 - conda install ERROR: No module Named "gseapy.gse"

Issue - State: closed - Opened by zqfang almost 2 years ago
Labels: question

#159 - Why I can't draw dotplot with prerank example?

Issue - State: closed - Opened by MugenQin almost 2 years ago - 4 comments

#158 - prerank input

Issue - State: closed - Opened by wangjiawen2013 almost 2 years ago - 1 comment

#154 - Handling multiple classes (and FDR)

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

#153 - Exeption: Error analyzing gene list

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

#152 - gmt file

Issue - State: closed - Opened by pengyan19 about 2 years ago - 1 comment

#151 - Logging.__init__() got an unexpected keyword argument 'text_color'

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

#150 - dotplot Error in line 396 in plot.py

Issue - State: closed - Opened by solo7773 about 2 years ago - 1 comment

#149 - ParserError: Too many columns specified: expected 4 and found 1 for Biomart

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

#148 - Fix t-test always returns 1e9 FDR

Pull Request - State: closed - Opened by Pearcekieser about 2 years ago - 6 comments

#147 - How can I produce gsea reports for positive and negative for cytoscape?

Issue - State: closed - Opened by daschukds about 2 years ago - 5 comments
Labels: New Feature, done

#145 - Apply `black` and `isort`

Pull Request - State: closed - Opened by cthoyt over 2 years ago - 5 comments

#144 - issue with biomart

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

#142 - Memory leak

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