Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / zqfang/GSEApy issues and pull requests

#154 - Handling multiple classes (and FDR)

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

#153 - Exeption: Error analyzing gene list

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

#152 - gmt file

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

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

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

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

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

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

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

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

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

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

Issue - State: closed - Opened by daschukds over 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 almost 3 years ago - 1 comment

#142 - Memory leak

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

#141 - corrected calculation of t_test

Pull Request - State: closed - Opened by pirakd almost 3 years ago - 1 comment

#140 - Confusion regarding phenotype permutation

Issue - State: closed - Opened by pirakd almost 3 years ago - 4 comments

#139 - Permission error connecting to Enrichr

Issue - State: closed - Opened by amcgarvey about 3 years ago - 2 comments

#138 - fixed biomart typo

Pull Request - State: closed - Opened by fairliereese about 3 years ago

#134 - Prerank step takes an incredible volume of memory

Issue - State: closed - Opened by PeifengJi about 3 years ago - 3 comments

#133 - NES values - error in calculations ?

Issue - State: closed - Opened by Floreuzan about 3 years ago - 1 comment
Labels: discussion

#131 - cannot import name 'gseaplot' from 'gseapy.plot'

Issue - State: closed - Opened by yhan8 about 3 years ago - 1 comment

#130 - Update enrichr.py

Pull Request - State: closed - Opened by engelsdaniel about 3 years ago - 1 comment

#129 - Improve offline enrichr mode

Pull Request - State: closed - Opened by engelsdaniel about 3 years ago - 1 comment

#126 - Update introduction.rst

Pull Request - State: closed - Opened by meereeum over 3 years ago

#125 - GSEA ES and NES values are nan

Issue - State: closed - Opened by rraadd88 over 3 years ago - 10 comments

#124 - Potential issue of floating point precision in prerank

Issue - State: closed - Opened by hsiaoyi0504 over 3 years ago - 4 comments

#123 - update human background gene

Pull Request - State: closed - Opened by hsiaoyi0504 over 3 years ago - 3 comments

#121 - Background gene is not saved in self._bg correctly and seems not be used

Issue - State: closed - Opened by hsiaoyi0504 over 3 years ago - 4 comments

#120 - Prerank input question

Issue - State: closed - Opened by hsiaoyi0504 over 3 years ago - 3 comments

#119 - I can't make dotplot graphs when I analyze more than one set

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

#118 - KeyError with plot.dotplot

Issue - State: closed - Opened by evcon131 over 3 years ago - 3 comments

#117 - GSEApy Exception: Error analyzing gene list

Issue - State: closed - Opened by Wendy-k2 over 3 years ago - 7 comments

#116 - GSEApy "KeyError: 'Adjusted P-value'"

Issue - State: closed - Opened by bromleyjd over 3 years ago - 1 comment

#112 - Fix Enrichr API

Pull Request - State: closed - Opened by fvalle1 over 3 years ago - 1 comment

#111 - Enrichr API key error

Issue - State: closed - Opened by t-silvers over 3 years ago - 4 comments

#110 - URL for enrichr libraries moved

Issue - State: closed - Opened by pcahan1 over 3 years ago - 12 comments

#109 - local mode, passing a dict as gene set, return no hit

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

#108 - ssgsea function cause "Invalid IHDR data" error

Issue - State: closed - Opened by afukada-cloud almost 4 years ago - 5 comments

#107 - enrichr doesn't show all the gene sets

Issue - State: closed - Opened by xiaojun-min about 4 years ago - 1 comment

#106 - KeyError: 'Adjusted P-value' when running enrichr

Issue - State: closed - Opened by erwinerdem about 4 years ago - 6 comments

#104 - error condition causes juypter notebook to hang

Issue - State: closed - Opened by AEDWIP over 4 years ago - 1 comment

#103 - what is the difference between prerank and single sample

Issue - State: closed - Opened by AEDWIP over 4 years ago - 3 comments

#102 - Ranking by absolute value of signal to noise

Issue - State: closed - Opened by caleb-lindgren over 4 years ago - 3 comments

#101 - ssGSEA leading edge

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

#100 - Maybe a bug: samples in the heatmap were less than expected

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

#99 - Suggestion of new features

Issue - State: open - Opened by loganylchen over 4 years ago - 1 comment
Labels: enhancement, New Feature

#98 - Inconsistent get_library_name and gp.enrichr for Yeast database

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

#97 - Repeat the whole python file the same times as many processes I set

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

#96 - Help using GSEApy for things other than genes

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

#95 - Inconsistent results

Issue - State: closed - Opened by boiarsky18 over 4 years ago - 1 comment

#93 - Citing your software

Issue - State: closed - Opened by ColtonGarelli over 4 years ago - 1 comment

#92 - Parallelism fix to reduce errors on large datasets like scRNAseq

Pull Request - State: closed - Opened by TheAustinator over 4 years ago - 2 comments

#89 - several question in using GSEApy

Issue - State: closed - Opened by Gin-Wang almost 5 years ago - 6 comments

#80 - Prerank empties out the dictionary

Issue - State: closed - Opened by jolespin over 5 years ago - 4 comments

#76 - ssgsea fails with pandas multiindex

Issue - State: closed - Opened by ac3957 over 5 years ago - 2 comments

#72 - enrichment test for two ranked gene lists

Issue - State: closed - Opened by MingBit over 5 years ago - 1 comment

#70 - the value of nes，pvalue and fdr can‘t achieve reproducibility

Issue - State: closed - Opened by huchua over 5 years ago - 2 comments

#68 - conda dockerfile

Issue - State: closed - Opened by moxgreen over 5 years ago - 1 comment

#55 - gseapy.prerank - errors for small ranked lists

Issue - State: closed - Opened by michaelpierrelee about 6 years ago - 8 comments
Labels: discussion

#51 - odd memory behavior use multiple processes

Issue - State: closed - Opened by ghost over 6 years ago - 2 comments
Labels: help wanted

#47 - expected enrichment score of -0.5, got -0.496 instead

Issue - State: closed - Opened by ghost over 6 years ago - 6 comments

#46 - y-axis in enrichment score plot is all zeros

Issue - State: closed - Opened by ghost over 6 years ago - 1 comment

#38 - A small question about the original GSEA implementation

Issue - State: closed - Opened by iseekwonderful almost 7 years ago - 2 comments

#19 - ValueError: Length of values does not match length of index

Issue - State: closed - Opened by segelmichael about 8 years ago - 6 comments
Labels: question