saezlab/decoupleR issues and pull requests

#103 - How to deal with gene readouts that are biased by gene length?

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

#102 - get_collectri ignores organism parameter setting

Issue - State: closed - Opened by woblkilr 12 months ago - 4 comments

#101 - Update README.md

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

#100 - Are TPMs better than counts for the linear model?

Issue - State: closed - Opened by andreyurch almost 1 year ago - 1 comment

#99 - GSEA_analysis

Issue - State: closed - Opened by mms100 about 1 year ago - 7 comments

#98 - Network is empty after intersecting it with mat

Issue - State: closed - Opened by JinSooJoo about 1 year ago - 8 comments

#97 - Error in `map2()`

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

#96 - Interpretation of TF Activity

Issue - State: closed - Opened by lizzyjoan about 1 year ago - 2 comments
Labels: question

#95 - get_collectri error

Issue - State: closed - Opened by t1nnenissen about 1 year ago - 5 comments

#94 - Prepare for upcoming Seurat v5 release

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

#93 - Pamgene S100 values to t-values

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

#92 - how to compute the pathway activity score for the pathway if I do not have the pathway genes weight

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

#91 - progeny vs decoupleR packages: which scores are trustworthy?

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

#90 - Can't fetch Dorothea regulons

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

#89 - Input for bulk analysis: taking or not the log of the normalized counts?

Issue - State: closed - Opened by merlevede over 1 year ago - 3 comments
Labels: question

#87 - get_collectri orgaism="mouse" return "human"

Issue - State: closed - Opened by Pazuzzilla over 1 year ago - 10 comments
Labels: database/omnipath

#86 - rationale behind using limma for bulk RNAseq TF inference?

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

#85 - Error when running run_wmean for transcription factor activity inference

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

#84 - How to understand the `weight` and `p_value` in the result of get_progeny.

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

#83 - get_collectri doesn't use organism argument

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

#82 - Fixed translation to mouse

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

#81 - Error: 'get_collectri' is not an exported object from 'namespace:decoupleR'

Issue - State: closed - Opened by hiiiyilingzhang over 1 year ago - 13 comments

#79 - Error in `convert_f_defaults()`:

Issue - State: closed - Opened by beetlejuice007 over 1 year ago - 4 comments

#78 - get_dorothea return an error with latest version of dplyr

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

#76 - Differences between two ways of getting dorothea database

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

#75 - Omnipath not accessible with get_resource()

Issue - State: closed - Opened by quyaingo over 1 year ago - 2 comments
Labels: database/omnipath

#74 - genes vf tf heatmap

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

#73 - added get_KSN_omnipath function

Pull Request - State: closed - Opened by adugourd over 1 year ago - 9 comments

#72 - mutate error when downloading dorothea

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

#71 - colinearity

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

#70 - Equivalent variable of t-value from limma in Deseq2 generated DEGs results

Issue - State: closed - Opened by Diennguyen8290 over 1 year ago - 2 comments

#69 - Error in mutate() when running get_dorothea()

Issue - State: closed - Opened by dano602 over 1 year ago - 2 comments

#68 - Discrepancy TF-Target database downloaded from DoRothEA and decoupleR

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

#67 - Using decoupleR across conditions

Issue - State: closed - Opened by singhh5050 almost 2 years ago - 3 comments
Labels: question

#66 - Fix mlm multicond

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

#65 - Issue with Omnipath retrieving data

Issue - State: closed - Opened by jsangalang almost 2 years ago - 3 comments
Labels: database/omnipath

#64 - Issue when running large dataset

Issue - State: closed - Opened by cnk113 almost 2 years ago - 1 comment

#63 - Error in parse(text = elt)

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

#62 - GSVA error

Issue - State: closed - Opened by tonyjhlam about 2 years ago - 2 comments
Labels: bug

#61 - Issues retrieving data from PROGENy using decoupleR & OmintpathR

Issue - State: closed - Opened by Vicbcn2001 about 2 years ago - 3 comments
Labels: database/omnipath

#60 - Gene expression and TF activity

Issue - State: closed - Opened by parkjooyoung99 over 2 years ago - 1 comment
Labels: question

#59 - Cannot fit a linear model with colinear covariables

Issue - State: closed - Opened by roskcl over 2 years ago - 1 comment
Labels: question

#58 - Options to use locally downloaded database

Issue - State: closed - Opened by woaidangyang over 2 years ago - 2 comments
Labels: question

#57 - Error in open.connection(con, "rb") Timeout was reached

Issue - State: closed - Opened by kaizen89 over 2 years ago - 10 comments

#56 - Inconsistent condition values in the decouple function output

Issue - State: closed - Opened by vntasis over 2 years ago - 1 comment
Labels: bug

#55 - Not a bug or an error, just wondering about the p-values from the inference.

Issue - State: closed - Opened by harimchun over 2 years ago - 2 comments
Labels: enhancement

#54 - Vignette build fails due to missing packages

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

#53 - `tidyverse` in `Suggests` and vignettes

Issue - State: closed - Opened by deeenes over 2 years ago - 1 comment
Labels: enhancement

#52 - Run_viper error

Issue - State: closed - Opened by Chengwei94 over 2 years ago - 2 comments

#51 - Can I still use Findmarkers on dorothea results returned by wmean

Issue - State: closed - Opened by Chengwei94 over 2 years ago - 1 comment
Labels: question

#50 - problems running get_progeny after conda install

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

#49 - adding regularization options to mlm - FZ

Pull Request - State: closed - Opened by fanzheng10 over 2 years ago

#48 - Error: Column `condition` not found in `.data`

Issue - State: closed - Opened by charlotteboys almost 3 years ago - 2 comments

#47 - Duplicated regulons in mlm after filtering

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

#46 - ulm, mlm, mdt and udt now accept matrices with one column as input

Pull Request - State: closed - Opened by PauBadiaM almost 3 years ago