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0
votes
0
replies
1.2k
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
2.8 years ago
yao hua
• 0
2
votes
8
replies
2.2k
views
Help with inspecting DEs from QLF test and LRT
edgeR
2.8 years ago
Tanner
• 0
2
votes
4
replies
3.2k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Christopher
• 0
0
votes
2
replies
1.9k
views
Why is my log fold change not centered around 0 and lower?
DESeq2
MAplot
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
Michael
• 0
0
votes
2
replies
2.3k
views
Download package ' org.Hs.eg.db 'when a problem emerged
org.Hs.eg.db
updated 2.8 years ago by
harish
• 0 • written 2.8 years ago by
996212796
• 0
1
vote
1
reply
1.3k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
greta
• 0
0
votes
4
replies
3.9k
views
DESeq2 and heatmap for multiple comparisons
DESeq2
2.8 years ago
artem.vorobyev
• 0
0
votes
1
reply
4.8k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
bio.boi
• 0
0
votes
2
replies
931
views
logFoldChange results in inverted comparison
#DESeq2
#LFC
#RNAseq
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
giulia.lopatriello
• 0
6
votes
12
replies
3.1k
views
Error when loading DMRcate
DMRcate
2.8 years ago
Bazingastats
• 0
0
votes
1
reply
1.6k
views
part of the volcano plot does not appear.
plot
volcano
volcanoplot
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
Sooni
▴ 10
0
votes
0
replies
1.4k
views
Problem with loading rtracklayer
rtracklayer
updated 2.8 years ago by
shepherl
4.2k • written 2.8 years ago by
jiahe.janet
• 0
0
votes
1
reply
1.0k
views
Installation of SingleR fails with GCC 8.2.0, Centos 7 - XPtr(Rcpp::Vector<19>::Proxy)
SimpleR
updated 2.7 years ago by
Jovana Maksimovic
▴ 20 • written 2.8 years ago by
cisbio
• 0
0
votes
0
replies
973
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
2.8 years ago
therealgenna
• 0
2
votes
2
replies
2.9k
views
Input for MAST
MAST
2.8 years ago
zuljiamel1991
▴ 10
0
votes
0
replies
760
views
XCMS normalization
xcms
2.8 years ago
T.RU
• 0
0
votes
5
replies
1.8k
views
What happens to genes with low dispersion during dispersion shrinkage in DESeq2
DESeq2
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
a.puchkina
• 0
1
vote
5
replies
2.1k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
Michael Steinbaugh
▴ 90
0
votes
0
replies
876
views
Multiple way network preservation
wgcna
2.8 years ago
madzayasodara
• 0
0
votes
14
replies
3.4k
views
Trouble downloading dada2
dada
dada2
2.8 years ago
elliottchon97
• 0
0
votes
4
replies
1.7k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
2.8 years ago
Dr.
• 0
0
votes
0
replies
783
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.8 years ago
Gilles
• 0
0
votes
2
replies
1.2k
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
2.8 years ago
fatemeh.peimani
• 0
0
votes
1
reply
1.2k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 2.8 years ago by
Rory Stark
★ 5.2k • written 2.9 years ago by
Hadar
• 0
0
votes
1
reply
999
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
updated 2.8 years ago by
Rory Stark
★ 5.2k • written 2.8 years ago by
slrpatty
• 0
1
vote
6
replies
3.0k
views
PlotCounts DESeq2 - how to plot count s for specific samples?
DESeq2
PlotCounts
2.8 years ago
annamariabugaj
▴ 10
0
votes
2
replies
4.6k
views
Conducting pair-wise comparison in DESeq2?
DESeq2
deseq2
biocondu
Bioconductor
RNASeq
written 2.8 years ago by
Hussain
• 0
6
votes
11
replies
2.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR
DifferentialExpression
limma
design
RNASeq
2.8 years ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
1.6k
views
snpsBySeqname() and snpsByOverlaps() functions in BSgenome package did not work in my computer
BSgeome
2.8 years ago
sunyingkai
• 0
0
votes
3
replies
1.6k
views
GSVA: Error loading interactive web app
igsva
GSVA
updated 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
sharvari gujja
▴ 40
2
votes
2
replies
1.1k
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
jtobias
▴ 10
3
votes
3
replies
1.5k
views
Incremental Write
append
rhdf5
2.8 years ago
kpalmer
▴ 10
0
votes
0
replies
1.2k
views
DMR.plot "Error: Too many stacks to draw"
DMRcate
Gviz
GV
2.8 years ago
gilliangoobie
• 0
2
votes
2
replies
1.4k
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
2.8 years ago
Hatchet
• 0
0
votes
0
replies
647
views
Visualize blastx output in R
blast
2.8 years ago
kvigil
• 0
2
votes
2
replies
1.1k
views
DE Analysis on cells from a patient derived mouse xenograft with high levels of mouse count "contamination"
DESeq2
2.8 years ago
jropa
▴ 10
0
votes
1
reply
1.2k
views
Differential expression analysis with global differences among samples (tissues)
DESeq2
qsmooth
edgeR
limma
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Gregory
• 0
0
votes
1
reply
1.8k
views
Extract Intersection Values from Venn
R
Venn
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
Dr.
• 0
2
votes
4
replies
1.6k
views
Question about GWASTools gdsSubset
GWASTools
gdsSubset
written 2.8 years ago by
SuperD
• 0
2
votes
6
replies
2.8k
views
DMRcate
DMRcate
R
DMRcatedata
Markdown
2.8 years ago
yr542
• 0
0
votes
2
replies
863
views
Does DESeq2 work for investigating the gene differential expression before and after the treat but in the same sample?
DESeq2
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
Sep
• 0
1
vote
2
replies
4.6k
views
DESeq2::plotPCA()
DESeq2
2.8 years ago
Kai Hu
▴ 70
0
votes
0
replies
675
views
installing flowPloidy
flowPloidyData
flowPloidy
2.8 years ago
Punn
• 0
0
votes
2
replies
1.1k
views
Error message trying to open downloaded package
error
DEP
2.8 years ago
kcpaul168
• 0
1
vote
1
reply
1.4k
views
Pseudobulk running all groups together vs subsetting first
DESeq2
edgeR
SingleCell
updated 2.8 years ago by
Wolfgang Huber
★ 13k • written 2.8 years ago by
nhaus
▴ 70
0
votes
0
replies
1.2k
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
2.8 years ago
ginie.dub
• 0
0
votes
6
replies
1.7k
views
Non windows utility for CEL file Binary to Ascii format conversion
written 19.3 years ago by
Lakshmanan Iyer
▴ 250
2
votes
2
replies
986
views
fomulation of contrasts for blocked design
edgeR
2.8 years ago
chaco001
• 0
0
votes
4
replies
1.1k
views
Load templates from openPrimeR
PCRmultiplex
openPrimeR
2.8 years ago
Santiago Edilberto
• 0
0
votes
1
reply
1.2k
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
2.8 years ago
Jenny Drnevich
★ 2.0k
46,692 results • Page
62 of 934
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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