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r
•
reset
0
votes
0
replies
16
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
2 days ago
osieman52
• 0
0
votes
1
reply
37
views
Change my bedgraph file to wig in R
bedgraph
R
wig
updated 4 days ago by
ATpoint
★ 1.4k • written 4 days ago by
margo
• 0
0
votes
1
reply
92
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 10 days ago by
Gordon Smyth
46k • written 11 days ago by
mfaleevs
• 0
4
votes
4
replies
191
views
Convert an R data.frame to a bed file in R
rtracklayer
R
bed
15 days ago • updated 11 days ago
L
• 0
4
votes
2
replies
150
views
good-first-issue (or similar) GitHub
Culture
R
GitHub
updated 24 days ago by
Michael Love
37k • written 24 days ago by
BioInfoBeginnerrr
• 0
0
votes
2
replies
155
views
DESeq2 analysis has not been run for this contrast
R
DiffBind
26 days ago
Wang
• 0
0
votes
2
replies
174
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 5 weeks ago by
ac.mainul.mmb
• 0
1
vote
0
replies
87
views
Mapping patient dataset onto control dataset
Cytometry
R
Data
5 weeks ago
hamiltond
▴ 10
0
votes
6
replies
354
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
6 weeks ago • updated 5 weeks ago
Mohamed
• 0
0
votes
4
replies
222
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
7 weeks ago • updated 6 weeks ago
Mohamed
• 0
2
votes
9
replies
344
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
94
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
150
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
319
views
Limma vs deseq2 results
limma
RNASeq
R
10 weeks ago
k___
▴ 20
2
votes
3
replies
258
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
170
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 1.4k • written 11 weeks ago by
Dimitris
• 0
3
votes
3
replies
226
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 11 weeks ago by
Gordon Smyth
46k • written 11 weeks ago by
mohammedtoufiq91
▴ 10
0
votes
6
replies
266
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
11 weeks ago
nabiyogesh
▴ 10
1
vote
2
replies
234
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
219
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 12 weeks ago by
Gordon Smyth
46k • written 12 weeks ago by
margo
• 0
4
votes
6
replies
326
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
12 weeks ago • updated 11 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
207
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
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
3
replies
620
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
901
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
3 months ago
kieran.short
▴ 30
0
votes
11
replies
599
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData
r
3 months ago
Mohamed
• 0
1
vote
3
replies
249
views
GVIZ giving error with loading hg38 genome
R
Gviz
3 months ago
RUser743
• 0
2
votes
1
reply
150
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
353
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
0
votes
7
replies
378
views
Which Limma guide is recommended ?
limma
R
DifferentialExpression
3 months ago
JAcky
• 0
0
votes
3
replies
240
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
163
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
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
1
reply
423
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
336
views
Ensembl non responsive
ensembl
R
4 months ago
ksci
▴ 10
0
votes
1
reply
401
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
216
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
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
590
views
R package installation error
HPC
R
Bioconducter
4 months ago
nabiyogesh
▴ 10
0
votes
0
replies
255
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
227
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
286
views
motifStack Plotting the correct data positions on x axis
motifStack
R
5 months ago
Marwah
• 0
0
votes
2
replies
659
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
8
replies
442
views
error in RnBeads installation
Epigenetics
RnBeads
R
5 months ago • updated 4 months ago
nabiyogesh
▴ 10
0
votes
2
replies
401
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
327
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
6 months ago
Hasan Alanya
• 0
0
votes
0
replies
128
views
Error in DEqMS proteomics analysis
DEqMS
R
DifferentialExpression
6 months ago
Mrinal.singh06
• 0
0
votes
0
replies
161
views
WGCNA with large Methylation matrix
wgcna
R
WGCNA
Methylation
6 months ago
Lorenzo
• 0
50 results • Page
1 of 1
Recent ...
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Comment: IsoformSwitchAnalyzeR package on mouse data
by
bpshtiwan
▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Comment: Design and contrast matrices for analyzing the effect of two factors of interest
by
Gordon Smyth
46k
I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
Comment: error running UniProt.ws
by
James W. MacDonald
60k
Or maybe it is a quick fix! Nicely done Marcel!
Answer: Error with TCGA package - TCGAbiolinks
by
Tiago C. Silva
▴ 220
It is working with the github version. Could you update please? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") …
Comment: Error with TCGA package - TCGAbiolinks
by
Marcel Ramos
570
You can try the Genomic Data Commons Data Portal at [https://portal.gdc.cancer.gov/][1] or the `GenomicDataCommons` R/Bioconductor packag…
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
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46k
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