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r
•
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0
votes
0
replies
22
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
5 days ago
osieman52
• 0
0
votes
1
reply
50
views
Change my bedgraph file to wig in R
bedgraph
R
wig
updated 7 days ago by
ATpoint
★ 1.4k • written 7 days ago by
margo
• 0
0
votes
1
reply
95
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 13 days ago by
Gordon Smyth
46k • written 14 days ago by
mfaleevs
• 0
4
votes
4
replies
201
views
Convert an R data.frame to a bed file in R
rtracklayer
R
bed
18 days ago • updated 14 days ago
L
• 0
4
votes
2
replies
151
views
good-first-issue (or similar) GitHub
Culture
R
GitHub
updated 27 days ago by
Michael Love
37k • written 27 days ago by
BioInfoBeginnerrr
• 0
0
votes
2
replies
160
views
DESeq2 analysis has not been run for this contrast
R
DiffBind
29 days ago
Wang
• 0
0
votes
2
replies
178
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression
GeneExpression
R
enrichment
DEGseq
updated 5 weeks ago by
swbarnes2
★ 1.1k • written 6 weeks ago by
ac.mainul.mmb
• 0
1
vote
0
replies
89
views
Mapping patient dataset onto control dataset
Cytometry
R
Data
6 weeks ago
hamiltond
▴ 10
0
votes
6
replies
380
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
6 weeks ago
Mohamed
• 0
0
votes
4
replies
223
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
8 weeks ago • updated 7 weeks ago
Mohamed
• 0
2
votes
9
replies
348
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
8 weeks ago • updated 7 weeks ago
Peipei
• 0
1
vote
1
reply
97
views
roughDispEstimate and momentsDispEstimate
estimator
roughmethodofmoments
DESeq2
R
Code
updated 8 weeks ago by
Basti
▴ 390 • written 8 weeks ago by
stew
• 0
0
votes
2
replies
152
views
R Bioconductor package Affxparser keeps crashing
affxparser
r
Bioconductor
updated 9 weeks ago by
James W. MacDonald
60k • written 9 weeks ago by
Cameron
• 0
3
votes
3
replies
332
views
Limma vs deseq2 results
limma
RNASeq
R
11 weeks ago • updated 10 weeks ago
k___
▴ 20
2
votes
3
replies
260
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R
edgeR
updated 11 weeks ago by
Gordon Smyth
46k • written 11 weeks ago by
Mohamed
• 0
1
vote
1
reply
175
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 12 weeks ago by
ATpoint
★ 1.4k • written 12 weeks ago by
Dimitris
• 0
3
votes
3
replies
227
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 12 weeks ago by
Gordon Smyth
46k • written 12 weeks ago by
mohammedtoufiq91
▴ 10
0
votes
6
replies
270
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
12 weeks ago
nabiyogesh
▴ 10
4
votes
6
replies
328
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
3 months ago • updated 12 weeks ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
242
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
12 weeks ago • updated 11 weeks ago
takemoto
• 0
1
vote
1
reply
222
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 12 weeks ago by
Gordon Smyth
46k • written 3 months ago by
margo
• 0
0
votes
1
reply
155
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport
R
updated 3 months ago by
Michael Love
37k • written 3 months ago by
cthangav
• 0
0
votes
1
reply
212
views
trouble installing DESeq2
install
packages
R
DESeq2
updated 3 months ago by
shepherl
3.2k • written 3 months ago by
eruan1
• 0
0
votes
3
replies
636
views
Problem with gcc/fortran compilers in new version of Bioconductor (Mac M1)
biocmanager
R
gofortran
Bioconductor
3 months ago
Olivia
• 0
5
votes
3
replies
930
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
3 months ago
kieran.short
▴ 30
5
votes
14
replies
2.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 3 months ago by
ATpoint
★ 1.4k • written 4.1 years ago by
Beginner
▴ 50
0
votes
11
replies
601
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData
r
3 months ago
Mohamed
• 0
1
vote
3
replies
250
views
GVIZ giving error with loading hg38 genome
R
Gviz
3 months ago
RUser743
• 0
0
votes
7
replies
381
views
Which Limma guide is recommended ?
limma
R
DifferentialExpression
4 months ago • updated 3 months ago
JAcky
• 0
2
votes
1
reply
155
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell
R
OSCA
updated 3 months ago by
jeroen.gilis
▴ 70 • written 3 months ago by
BioInfoBeginnerrr
• 0
1
vote
5
replies
356
views
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
clusterProfiler
r
updated 3 months ago by
Guido Hooiveld
★ 3.3k • written 3 months ago by
Paul
• 0
22
votes
14
replies
2.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 3 months ago by
Neri0304
• 0 • written 4 months ago by
Dina
▴ 50
0
votes
3
replies
242
views
lfcShrink contrast
lfcshrink
R
DESeq2
updated 4 months ago by
ATpoint
★ 1.4k • written 4 months ago by
LHA_trash
• 0
0
votes
0
replies
167
views
Job:
Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology
clinical
R
bioinformatics
multiomics
oncology
4 months ago
vincent.piras
• 0
0
votes
1
reply
429
views
How can i download maf files form GDC Data Portal?
maf
R
updated 4 months ago by
Kevin Blighe
3.6k • written 4 months ago by
misslubblys
• 0
2
votes
3
replies
340
views
Ensembl non responsive
ensembl
R
4 months ago
ksci
▴ 10
0
votes
1
reply
413
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
updated 4 months ago by
Tiago C. Silva
▴ 220 • written 4 months ago by
spyrouglykeria
• 0
3
votes
2
replies
218
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
4 months ago • updated 3 months ago
Dakarai
▴ 10
0
votes
2
replies
674
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 4 months ago by
kent.riemondy
• 0 • written 5 months ago by
svenbioinf
• 0
0
votes
1
reply
151
views
Error running hierClust
hierClust
R
SNPs
clustering
updated 4 months ago by
James W. MacDonald
60k • written 4 months ago by
sekhwal
• 0
0
votes
0
replies
141
views
normalisation options in RnBeads
Epigenetics
RnBeads
R
Bioconducter
4 months ago
nabiyogesh
▴ 10
4
votes
8
replies
593
views
R package installation error
HPC
R
Bioconducter
4 months ago
nabiyogesh
▴ 10
0
votes
0
replies
261
views
How to pool phyloseq data?
phyloseq
r
updated 4 months ago by
Michael Love
37k • written 4 months ago by
strep
• 0
1
vote
3
replies
229
views
Identifying DEG between development stages
plant
Transcriptomics
DESeq2
r
updated 5 months ago by
Basti
▴ 390 • written 5 months ago by
cicely.day
• 0
4
votes
4
replies
289
views
motifStack Plotting the correct data positions on x axis
motifStack
R
5 months ago
Marwah
• 0
0
votes
8
replies
448
views
error in RnBeads installation
Epigenetics
RnBeads
R
5 months ago • updated 4 months ago
nabiyogesh
▴ 10
0
votes
2
replies
408
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux
R
tximport
5 months ago
nakane_clan
• 0
0
votes
1
reply
249
views
Running limma in parallel
parallel
R
limma
EWAS
updated 5 months ago by
Gordon Smyth
46k • written 5 months ago by
Lorenzo
• 0
2
votes
2
replies
330
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
6 months ago
Hasan Alanya
• 0
0
votes
0
replies
129
views
Error in DEqMS proteomics analysis
DEqMS
R
DifferentialExpression
6 months ago
Mrinal.singh06
• 0
50 results • Page
1 of 1
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Answer: mapToAlignments_issue
by
Hervé Pagès
15k
> I would expect in case of reverse alignment lifted ranges to correspond to position 91-100 of the query sequence. Nope. Local coordinate…
Answer: Problem related to `biomaRt::getBM()` during `R CMD check` execution
by
James W. MacDonald
60k
Does the section in the biomaRt vignette that talks about caching (and using a temp dir) help?
Comment: OPLS-DA: confidence interval for accuracy metric
by
Eddie
• 0
Worked well under pROC. Thank you
Comment: errors in annotation
by
James W. MacDonald
60k
If you go to NCBI and the data appear to be correct, then they have evidently already fixed the errors you have found. The data we download…
Comment: How should I set my eps value in cluster profiler?
by
Guido Hooiveld
★ 3.3k
Under the hood `clusterProfiler` makes use of a (fast) GSEA algorithm implemented in the package `fgsea` (function `fgseaMultilevel`). The …
Votes
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
How to select summit size for histone ChiP-Seq in Diffbind
Comment: GSEA with Wikipathways not entirely reproducible
Comment: How to get gene length for RPKM directly from DGEList object in latest edgeR?
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