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saezlab
/
transcriptutorial
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
https://saezlab.github.io/transcriptutorial/
GNU General Public License v3.0
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tried to add docs
#50
adugourd
closed
1 year ago
0
typo correction
#49
adugourd
closed
1 year ago
0
added network visualisation
#48
adugourd
closed
1 year ago
0
updated the tutorial from scratch
#47
adugourd
closed
1 year ago
0
04_TranscriptionFactor_activity_with_Dorothea issue with run_viper
#46
manas-kohli
opened
1 year ago
8
Got a problem using assignPROGENYScores
#45
Holmes815
closed
1 year ago
1
04_Dorothea_Volcano nice failing
#44
Camillula
closed
2 years ago
4
Comparing Cancer cell lines with normal tissues
#43
RzgarHosseini
closed
2 years ago
2
04_TranscriptionFactor_activity_with_Dorothea error in R script
#42
dilipgosar
closed
1 year ago
1
Transcriptorial 6: Enrichment analysis p-value errors
#41
CheyennedeVriend
closed
1 year ago
2
could not find function "magicPlotMakerLight"
#40
dilipgosar
closed
2 years ago
3
Unable to call runCarnival
#39
CheyennedeVriend
closed
2 years ago
7
download data automatically
#38
gabora
closed
1 year ago
1
fix #36
#37
gabora
closed
2 years ago
0
topTable returns 5 columns, but ttopFormatter expects 6
#36
gabora
closed
2 years ago
4
progenyMembers.RData can not load
#35
whiteorchid
closed
2 years ago
1
duplicate Node1 in CARNIVAL_result
#34
whiteorchid
closed
2 years ago
0
visNet visualization stack into one line
#33
whiteorchid
closed
2 years ago
0
How to use log2FC instead of NES in transcription factors analysis in Dorothea
#32
AmiraAlakhdar
closed
1 year ago
0
run CARNIVAL gives Error in Writing cplex command file
#31
anoopktiwari
closed
1 year ago
0
could not find function "extractCARNIVALnodes"
#30
nattyht
closed
1 year ago
0
carnival_visNet visualization in part 05
#29
ulrmu
closed
1 year ago
4
Cplex solver in part 05
#28
clohoff
closed
1 year ago
6
Heatmap in part 04
#27
clohoff
closed
1 year ago
0
Packages for running CARNIVAL
#26
clohoff
closed
1 year ago
0
library(magrittr)
#25
clohoff
closed
1 year ago
0
Batch correction
#24
ulrmu
closed
3 years ago
5
Missing input file for part 6
#23
szsctt
closed
1 year ago
4
Error with top(100) in tutorial#3
#22
asumann
closed
1 year ago
5
Enrichment Analysis significance cutoff
#21
Semple-bio
closed
1 year ago
0
Shared interactions figure
#20
Semple-bio
closed
3 years ago
1
Progeny with permutations changes CARNIVAL results each time
#19
IvanEllson
closed
3 years ago
3
PROGENy and DoRothEA enrichment p-values
#18
ojziff
closed
1 year ago
1
mouse data
#17
Semple-bio
closed
1 year ago
3
Results of TF activites
#16
Semple-bio
closed
3 years ago
4
Using DE results from DESeq2
#15
gilbertlsk
closed
1 year ago
13
Does this method also apply to microarray data?
#14
sqianglan
closed
1 year ago
3
CARNIVAL memory error
#13
ojziff
closed
1 year ago
3
Error in sample_resolution_carnival.R obtaining tfList with larger ncol data
#12
IvanEllson
closed
3 years ago
1
Misuse NES in PROGENy zscores
#11
jperales
closed
1 year ago
1
Fix for Identifier Kung-Fu
#10
PauBadiaM
closed
3 years ago
1
Progeny documentation and tutorial script conflict
#9
IvanEllson
closed
3 years ago
3
Regarding of CARNIVAL installing
#8
hmkim
closed
3 years ago
5
Long running time of the sample_resolution_carnival.R script for producing carnival_sample_resolution.rds file from my own data
#7
sqianglan
closed
3 years ago
5
Proofreading of .Rmd files
#6
charlotteboys
closed
4 years ago
0
An error occurred while installing package 'bioconda::bioconductor-dorothea-1.0.0-r40_0'
#5
PauBadiaM
closed
3 years ago
9
Can't create conda enviroment
#4
PauBadiaM
closed
4 years ago
1
Ivanovaos patch 1
#3
rosherbal
closed
4 years ago
0
Shall we remove tex and html files from scripts folder?
#2
jperales
closed
4 years ago
1
Update FAQ_CARNIVAL.md
#1
ivanovaos
closed
4 years ago
0
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