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0
votes
0
replies
110
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago
nromerov
• 0
1
vote
3
replies
254
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by
Marcel Ramos
690 • written 5 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
122
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
5 weeks ago
mayra.haedo
• 0
0
votes
0
replies
109
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
5 weeks ago
taylor.witte
• 0
0
votes
0
replies
130
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
5 weeks ago
erbrocato
• 0
1
vote
4
replies
280
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
5 weeks ago
samuel.channon
• 0
0
votes
2
replies
196
views
Visium RNA
metaMSdata
updated 5 weeks ago by
vvvc360work2
• 0 • written 5 weeks ago by
Karlison
• 0
1
vote
2
replies
276
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
111
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
5 weeks ago
BID
• 0
1
vote
3
replies
266
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 4 weeks ago by
mercedeh.movassagh
▴ 10 • written 5 weeks ago by
María
• 0
0
votes
2
replies
231
views
Error in msaFun Cannot open input file. No alignment!
msa
written 6 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
191
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
Julie
• 0
0
votes
1
reply
172
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
236
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago
Sam
▴ 10
0
votes
1
reply
220
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 7 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
190
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago
red_bricks
▴ 50
0
votes
0
replies
130
views
FELLA plotGraph function won't change the legend
FELLA
7 weeks ago
yuhang
• 0
0
votes
0
replies
140
views
medips-output
ngsReports
MEDIPS
7 weeks ago
subhiksha
• 0
0
votes
0
replies
133
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
7 weeks ago
bocsci11
• 0
0
votes
0
replies
110
views
The graphical interface of FELLA doesn't work
FELLA
7 weeks ago
yuhang
• 0
0
votes
0
replies
129
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
7 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
147
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
7 weeks ago
Henry
• 0
0
votes
1
reply
210
views
Rcpp compilation error
Release
Rcpp
updated 7 weeks ago by
ATpoint
★ 4.1k • written 7 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
172
views
Rain error: invalid annotation of time points
rain
7 weeks ago
mpuli011
• 0
0
votes
0
replies
180
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
7 weeks ago
Felix
• 0
0
votes
0
replies
142
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
7 weeks ago • updated 6 weeks ago
Giovanni Calice
▴ 160
0
votes
0
replies
191
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
Andrew
• 0
0
votes
0
replies
136
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
8 weeks ago
chris2.a.white
• 0
0
votes
0
replies
150
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
8 weeks ago
jk
• 0
0
votes
0
replies
146
views
Can I combine collinear variables into a single value
BatchEffect
limma
8 weeks ago
Harrsha
• 0
0
votes
0
replies
222
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
8 weeks ago
vipul14
• 0
0
votes
0
replies
111
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
8 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
138
views
lfcSE
RGSEA
8 weeks ago
Gordon
• 0
0
votes
4
replies
287
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
8 weeks ago
mperalc
• 0
1
vote
0
replies
164
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
9 weeks ago
BioinfoMug
• 0
0
votes
0
replies
154
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
9 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
243
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 9 weeks ago by
ATpoint
★ 4.1k • written 9 weeks ago by
sodiogoes
• 0
0
votes
6
replies
693
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 7 weeks ago by
qianyi13
• 0 • written 9 weeks ago by
Pavel
• 0
0
votes
2
replies
308
views
problem in installing the new version of bioconductor
ANCOMBC
updated 9 weeks ago by
shepherl
3.8k • written 9 weeks ago by
Maryam
• 0
0
votes
0
replies
163
views
Comparing the effects of a condition over time in two seperate tissues
MAST
9 weeks ago
Dillon
• 0
0
votes
4
replies
335
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 9 weeks ago by
shepherl
3.8k • written 9 weeks ago by
Lucille
• 0
0
votes
3
replies
241
views
problems updating package
TrajectoryGeometry
9 weeks ago
michael.shapiro
• 0
0
votes
0
replies
201
views
how to solve this error?
ChAMPdata
ChAMP
10 weeks ago
Meghana
• 0
1
vote
1
reply
251
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 5 weeks ago by
SamGG
▴ 350 • written 10 weeks ago by
jarod
▴ 30
0
votes
0
replies
156
views
flowAI: flow rare check in R vs FlowJo
flowAI
10 weeks ago
Olena
• 0
0
votes
0
replies
193
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
10 weeks ago
mat149
▴ 70
0
votes
0
replies
162
views
GDC slides download
TCGAbiolinks
10 weeks ago
jain72744
• 0
0
votes
0
replies
211
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
10 weeks ago
Abril
• 0
0
votes
4
replies
287
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 10 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 11 weeks ago by
tirordep
• 0
0
votes
1
reply
213
views
"Counts" in enrichGO
GSEABase
updated 11 weeks ago by
Tyler Sagendorf
▴ 10 • written 11 weeks ago by
Matthew
• 0
1,000 results • Page
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Replies
Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
alserg
▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks Robert for an educative response!
Votes
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
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