Ecosyste.ms: Issues

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

GitHub / ctlab/fgsea issues and pull requests

#161 - Understandig GESECA results

Issue - State: closed - Opened by Teulip 2 months ago - 2 comments

#160 - Issue 150 plotCoregulationSpatial

Pull Request - State: closed - Opened by vdsukhov 3 months ago

#159 - How to prepare pathway used for fgsea function

Issue - State: closed - Opened by yulchen810 3 months ago - 5 comments

#158 - add rank plot for the GSEA plot

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

#157 - fora example in vignette

Pull Request - State: closed - Opened by markziemann 4 months ago - 1 comment

#156 - Adding fold enrichment score to fora() output

Pull Request - State: closed - Opened by markziemann 4 months ago - 1 comment

#155 - Understanding the scoreType

Issue - State: closed - Opened by alkurowska 6 months ago - 2 comments

#154 - GSEA to discover mixed enriched terms

Issue - State: closed - Opened by mauritsunkel 6 months ago - 5 comments

#153 - Implementation question

Issue - State: closed - Opened by mauritsunkel 7 months ago - 5 comments

#152 - Question: Geseca output, column "size"

Issue - State: closed - Opened by oswaldbra12 7 months ago - 4 comments

#150 - Support for multiple samples in plotCoregulationSpatial

Issue - State: closed - Opened by assaron 8 months ago

#149 - Error in preparePathwaysAndStats

Issue - State: closed - Opened by TX-Xiao 9 months ago - 5 comments

#148 - are there p-value calculated for each leading edge gene?

Issue - State: closed - Opened by Leran10 9 months ago - 2 comments

#147 - Try to understand how ES is calculated

Issue - State: closed - Opened by ghbore 9 months ago - 3 comments

#146 - Question: scaling size of spots

Issue - State: closed - Opened by jyoo19 10 months ago - 2 comments

#145 - Non-deterministic output with seed set, `nproc = 1`, and newest version

Issue - State: closed - Opened by chriswzou 10 months ago - 3 comments

#144 - fgsea giving identical padj values across many pathways

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

#143 - Gene filtering for FGSEA

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

#142 - Prepare for upcoming Seurat v5 release

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

#141 - github actions test

Pull Request - State: closed - Opened by assaron about 1 year ago

#140 - How to report for enriched gene sets?

Issue - State: closed - Opened by Close-your-eyes about 1 year ago - 2 comments

#139 - minSize and maxSize

Issue - State: closed - Opened by ag1805x over 1 year ago - 1 comment
Labels: question

#138 - fgseaMultilevelCpp doens't seem to be installed

Issue - State: closed - Opened by G3N0M3 over 1 year ago - 6 comments

#137 - Obtain per-sample expression value for a gene set

Issue - State: open - Opened by PatrickMaclean over 1 year ago - 1 comment

#135 - Insignificant p-values

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

#134 - Question: distribution requirements of statistics

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

#133 - Error in calcGseaStatCumulativeBatch

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

#132 - Will fgsea remove the wrong gene names in the input gene list?

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

#131 - Which genes should I use?

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

#130 - Does fGSEA require minSize as well?

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

#129 - Stats should be named

Issue - State: closed - Opened by been9312 over 1 year ago - 1 comment

#127 - Question: Visium Data and pulling out cells with high GO enrichment for a given pathway

Issue - State: open - Opened by DirtyHarry80 almost 2 years ago - 8 comments
Labels: question

#126 - Spatial Code Error in base::colSums

Issue - State: closed - Opened by DirtyHarry80 about 2 years ago - 5 comments

#125 - GESECA function not existing

Issue - State: closed - Opened by DirtyHarry80 about 2 years ago - 3 comments

#124 - Question: unbalanced gene-level statistic warning

Issue - State: closed - Opened by TatiKarp about 2 years ago - 7 comments
Labels: question

#123 - Question: about scoreType = 'pos'

Issue - State: closed - Opened by noblegasss about 2 years ago - 1 comment
Labels: question

#121 - Use outside of R

Issue - State: open - Opened by maxkfranz about 2 years ago - 4 comments

#120 - Questions related to fgsea algorithm

Issue - State: closed - Opened by lucolotto about 2 years ago - 1 comment
Labels: question

#119 - Subset of genes

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

#118 - New method: Gene Set Co-Regulation Analysis (geseca)

Pull Request - State: closed - Opened by vdsukhov about 2 years ago

#117 - is there a plan to implement fast ssGSEA?

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

#116 - Citation

Issue - State: open - Opened by pstew over 2 years ago - 3 comments

#115 - p.val threshold error in collapsePathways ()

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

#114 - A weird result: Highly enrichement visually but p value is not significant

Issue - State: closed - Opened by chent5 over 2 years ago - 6 comments

#113 - added more details about scoreType

Pull Request - State: closed - Opened by ShaiberAlon over 2 years ago - 1 comment

#112 - problem of fgseaMultilevel

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

#111 - Problematic p-value histogram from fgsea (scoreType='pos')

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

#110 - Results are not reproducible

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

#109 - Info on running multi-condition geseca

Issue - State: closed - Opened by kvittingseerup almost 3 years ago - 5 comments

#108 - enrichment score seems to have inverse sign

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

#107 - fgsea gives many highly sign. gene sets for comparison where I expect a few

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

#106 - p values

Issue - State: closed - Opened by davidlyon3 about 3 years ago - 3 comments

#104 - fgsea set.seed returns different results on bitbucket server than locally

Issue - State: closed - Opened by ldiao about 3 years ago - 5 comments

#103 - fgsea-simple vs fgsea-multilevel - when to use one or the other?

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

#101 - plotGseaTable not displaying the results

Issue - State: closed - Opened by RobertWhitener over 3 years ago - 13 comments

#100 - p values not reproducible when running fgsea function despite set.seed

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

#99 - Duplicated genes in $leadingEdge output from fgsea()

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

#98 - Error in pathway %fin% pathwaysToCheck : object 'pathway' not found

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

#97 - NA in pval column

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

#96 - direction of pathway change in the results

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

#95 - Ranking genes from Sleuth with aggregated p-value

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

#94 - multilevelImpl function fatal error

Issue - State: closed - Opened by mfrisoli126 over 3 years ago - 3 comments

#93 - fgsea hangs with nperm=1001, but not 1000

Issue - State: open - Opened by assaron over 3 years ago - 6 comments
Labels: invalid

#92 - the same results with descending and ascending order of gene list

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

#91 - Update .travis.yml

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

#90 - Update appveyor.yml

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

#89 - Error: Aesthetics must be either length 1 or the same as the data (1): x and xend

Issue - State: closed - Opened by yueli8 over 3 years ago - 1 comment

#88 - fgsea vs liger: what is the difference in the results?

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

#87 - scoreType argument

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

#86 - is there any way to output all results of all inputted pathways

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

#85 - Which testing method is the best?

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

#84 - Suggestion: multi-thread collapsePathways

Issue - State: open - Opened by Horokhovskyi about 4 years ago - 1 comment

#83 - p-value calculation using fgsea fgseaSimple function

Issue - State: closed - Opened by mengyuankan about 4 years ago - 10 comments

#82 - Error in if (maxP > -minP) { : missing value where TRUE/FALSE needed

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

#81 - fora call errors when no pathways overlap with universe

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

#80 - Different results on Mac and Linux

Issue - State: closed - Opened by korommatyi about 4 years ago - 5 comments

#79 - scoreType question

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

#78 - fgsea never stops running

Issue - State: closed - Opened by johnse about 4 years ago - 5 comments

#77 - How to calcuclate the error estimations in returned p-values?

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

#76 - collapsePathways

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

#74 - `theme_bw()` is hard-coded in some plots

Issue - State: closed - Opened by mjsteinbaugh over 4 years ago - 6 comments

#73 - Change the estimate of the probability of the denominator

Pull Request - State: closed - Opened by vdsukhov over 4 years ago

#72 - struggling to understand fgsea output

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

#71 - Fix a bug for the case when the signed ES = 0 and scoreType != std

Pull Request - State: closed - Opened by vdsukhov over 4 years ago - 1 comment

#70 - Identical padj among the top significant pathways

Issue - State: closed - Opened by trezende21 over 4 years ago - 1 comment

#69 - BPPARAM error

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

#68 - Cumulative test

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

#67 - fgsea NA values?

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

#66 - Ranking the genes from Seurat DE output file

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

#65 - Depends: Rcpp

Issue - State: closed - Opened by pcarbo over 4 years ago - 6 comments

#63 - Question about collapsePathways() logic

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

#50 - scRNA-seq: how to create the Ranked list?

Issue - State: open - Opened by asmariyaz23 over 5 years ago - 17 comments
Labels: question

#43 - Add option to plotGseaTable to return plot

Pull Request - State: closed - Opened by chrismiddleton over 5 years ago - 1 comment