saezlab decoupleR issues

saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.

https://saezlab.github.io/decoupleR/

GNU General Public License v3.0

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issues

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Subscript out of bounds error

#130 savagesr opened 3 weeks ago
7
get_progeny and organism = 'mouse' reports an error

#129 fedenichetti closed 3 weeks ago
2
get_progeny fails when using `organsim = "mouse"`

#128 Christian-Heyer closed 1 month ago
10
run_ulm taking very long to run and no feedback on progress

#127 gilstel closed 1 week ago
3
Can't get PROGENy model by get_progeny

#126 leeyangyangyang closed 1 month ago
7
GSVA error

#125 victorcat4 closed 1 week ago
1
added option to load meta data

#123 smuellerd closed 2 months ago
0
TF target genes in decoupleR analysis of scRNA-seq data

#122 JinSooJoo closed 2 months ago
3
Error in get_collectri()

#121 FoMooo closed 3 months ago
2
differential expression analysis and GSEA

#119 Sophon-0 opened 3 months ago
8
TF analysis between conditions scRNA

#118 kiwipeel closed 2 months ago
9
scRNA TF activity inference

#117 SofyaMa closed 4 months ago
2
High TF activity with few significant genes

#116 laurie-tonon closed 2 months ago
3
get_collectri is not able to fetch the right organism

#115 tamerbio closed 4 months ago
6
Transcription factor activity inference

#114 ramyavenk closed 4 months ago
2
Number of matched genes in pathway analysis

#113 kiwipeel closed 4 months ago
1
Pathway activity inference from scRNA-seq tutorial produces wrong results?

#112 kiwipeel closed 4 months ago
1
Question about TF activity inference analysis in single cell integrated datasets

#111 ChrisTzaferis closed 4 months ago
2
Problems to understand the analysis of the tutorial

#110 Gregjlt closed 4 months ago
3
get_collectri is hard coded for human

#109 karJac closed 6 months ago
2
Use FindAllMarkers to detect top TFs per cluster in scRNA data

#108 akramdi closed 5 months ago
1
Error after get_resource() and check_repeated_edges(network)

#107 sciotlos closed 5 months ago
2
TF activities in single-cell: `run_ulm` takes too long

#106 nicholaslimwy closed 6 months ago
2
Error: error in `str_to_upper()` OmnipathR

#105 maartenciers closed 7 months ago
2
DESeq2 input for Transcription factor activity inference in bulk RNA-seq

#104 t1nnenissen closed 5 months ago
1
How to deal with gene readouts that are biased by gene length?

#103 jgoldmann closed 7 months ago
2
get_collectri ignores organism parameter setting

#102 woblkilr closed 7 months ago
4
Update README.md

#101 adugourd closed 7 months ago
0
Are TPMs better than counts for the linear model?

#100 andreyurch closed 7 months ago
1
GSEA_analysis

#99 mms100 closed 7 months ago
7
Network is empty after intersecting it with mat

#98 JinSooJoo closed 8 months ago
8
Error in `map2()`

#97 noranekonobokkusu closed 8 months ago
2
Interpretation of TF Activity

#96 lizzyjoan closed 8 months ago
2
get_collectri error

#95 t1nnenissen closed 9 months ago
5
Prepare for upcoming Seurat v5 release

#94 Gesmira closed 2 months ago
0
Pamgene S100 values to t-values

#93 DuruTuncer closed 7 months ago
1
how to compute the pathway activity score for the pathway if I do not have the pathway genes weight

#92 FADHLyemen closed 8 months ago
4
progeny vs decoupleR packages: which scores are trustworthy?

#91 ismailelshimy closed 10 months ago
1
Can't fetch Dorothea regulons

#90 SophieGaiani closed 11 months ago
2
Input for bulk analysis: taking or not the log of the normalized counts?

#89 merlevede closed 10 months ago
3
get_collectri orgaism="mouse" return "human"

#87 Pazuzzilla closed 1 year ago
10
rationale behind using limma for bulk RNAseq TF inference?

#86 erzakiev closed 1 year ago
4
Error when running run_wmean for transcription factor activity inference

#85 TrmMelanoma closed 11 months ago
5
How to understand the `weight` and `p_value` in the result of get_progeny.

#84 xiangpin closed 11 months ago
1
get_collectri doesn't use organism argument

#83 majorkazer closed 1 year ago
2
Fixed translation to mouse

#82 smuellerd closed 1 year ago
0
Error: 'get_collectri' is not an exported object from 'namespace:decoupleR'

#81 hiiiyilingzhang closed 1 year ago
13
Error in `convert_f_defaults()`:

#79 hemantgujar closed 1 year ago
4
get_dorothea return an error with latest version of dplyr

#78 pedriniedoardo closed 1 year ago
2
Differences between two ways of getting dorothea database

#76 yunbokai closed 1 year ago
2