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DESeq2: Comparison between 1 test sample with 1 control sample
DESeq2
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
Vivek
• 0
20
votes
5
replies
11k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 3 months ago by
vs
• 0 • written 6.9 years ago by
shepherl
4.2k
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 2.6 years ago by
Wei Shi
★ 3.6k • written 2.6 years ago by
Carlos
• 0
0
votes
1
reply
1.5k
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 2.6 years ago by
Peter Hickey
▴ 760 • written 2.6 years ago by
sandra.garces.19
• 0
0
votes
1
reply
710
views
polyester biases
polyester
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Seongwoo Han
▴ 10
0
votes
3
replies
1.4k
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Alberto
• 0
2
votes
17
replies
3.4k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Alina
• 0
3
votes
5
replies
4.1k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
updated 4 months ago by
gunkata9454
• 0 • written 2.6 years ago by
Mark
▴ 10
0
votes
2
replies
855
views
Deseq2 design
DESeq2
genes
Differential
expressed
2.6 years ago
Syed Zaheer
▴ 10
1
vote
4
replies
1.4k
views
How to annotate mir4.1 arrays?
AffymetrixChip
miRNA
oligo
2.6 years ago • updated 2.4 years ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
2
replies
1.3k
views
DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2
DifferentialExpression
2.6 years ago
António Miguel de Jesus Domingues
▴ 510
2
votes
4
replies
3.2k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
2.6 years ago
Yijing
• 0
1
vote
2
replies
848
views
Contrast of Contrasts in Limma
limma
DifferentialExpression
2.6 years ago
mpitz
• 0
0
votes
3
replies
2.5k
views
Recount3 error with default "recount3_url" option
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
1.4k
views
Recount3 data download problem
recount
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
gamma.jian
▴ 10
2
votes
6
replies
2.2k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
Max Bone
• 0
2
votes
11
replies
2.8k
views
Not able to download recount3 data
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
Niveditha
▴ 20
0
votes
2
replies
1.3k
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.0 years ago by
dml
• 0
1
vote
3
replies
2.2k
views
DESeq2 1.40.0 binary install issue on Mac M1 (Bioconductor 3.17)
DESeq2
written 2.6 years ago by
MEME
▴ 10
0
votes
0
replies
1.0k
views
News:
RNA-seq analysis with Bioconductor Carpentries workshop, Boston, Jul 31-Aug 1
Bioconductor
Event
Community
Training
2.6 years ago
Maria Doyle
▴ 110
1
vote
3
replies
1.9k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
David
▴ 20
1
vote
11
replies
3.4k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 2.6 years ago by
Martin Morgan
25k • written 2.6 years ago by
Michael Steinbaugh
▴ 90
4
votes
4
replies
2.2k
views
S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconductor 3.17
S4Vectors
written 2.6 years ago by
Michael Steinbaugh
▴ 90
0
votes
2
replies
816
views
Developing new features
Rbowtie2
2.6 years ago
Franck RICHARD
• 0
0
votes
3
replies
1.2k
views
how to do splot with opls?
splots
updated 2.6 years ago by
shepherl
4.2k • written 2.6 years ago by
jing.yi
• 0
0
votes
0
replies
754
views
Getting the exon co-ordinates and location
exon
AnnotationHubData
2.6 years ago
mahima.g
• 0
2
votes
2
replies
970
views
load failed for ‘DESeq2’
DESeq2
updated 2.6 years ago by
shepherl
4.2k • written 2.6 years ago by
MEME
▴ 10
1
vote
3
replies
1.6k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower
edgeR
DifferentialExpression
limma
RNASeq
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Sara
• 0
0
votes
1
reply
909
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
Adam
• 0
0
votes
1
reply
944
views
custom annotations with annotatr
annotatr
2.6 years ago
luca.s
▴ 50
0
votes
0
replies
1.8k
views
PLSDA : No model was built because the first predictive component was already not significant.
plsda
2.6 years ago
MLF
• 0
3
votes
7
replies
2.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
2.6 years ago
Yijing
• 0
0
votes
0
replies
988
views
Volcano plot
limma
AffymetrixChip
2.6 years ago
e.gunaut
• 0
0
votes
4
replies
1.7k
views
Limma multi-group, nested analysis with aggregation
limma
2.6 years ago • updated 2.4 years ago
Jonathan
▴ 10
1
vote
1
reply
1.1k
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis
topGO
missMethyl
MethylationArrayData
MethylationArray
updated 2.6 years ago by
belinda.phipson
▴ 40 • written 2.6 years ago by
Grace
• 0
0
votes
1
reply
1.1k
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
qiz218591
• 0
8
votes
12
replies
3.8k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Michael Steinbaugh
▴ 90
0
votes
2
replies
2.5k
views
model matrix not full rank
DESeq2
RNASeq
updated 2.6 years ago by
garryfrenchgarry
• 0 • written 2.6 years ago by
Simran
• 0
0
votes
2
replies
808
views
ANOVA-like testing for bulkRNAseq with three conditions with Wald test
DESeq2
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
600
views
calculating effect of condition taking into account patient origin and clone_origin
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
idetoma
• 0
1
vote
2
replies
818
views
Wondering if DESeq2 is appropriate for PhIP-seq data?
DESeq2
PhIP-seq
2.6 years ago
Samantha
• 0
0
votes
1
reply
1.0k
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2
RNASeq
updated 2.6 years ago by
Michael Love
43k • written 2.7 years ago by
rohanphn
• 0
0
votes
0
replies
938
views
How to speed up pileup from Rsamtools?
Rsamtools
pileup
2.6 years ago
alexandr.gopanenko
▴ 50
1
vote
4
replies
8.7k
views
Error loading impute(): '/usr/lib/libgfortran.5.dylib' (no such file)
Install
impute
updated 2.6 years ago by
yuzhijian
• 0 • written 3.8 years ago by
Aaron
• 0
0
votes
1
reply
1.5k
views
DESeq2 Results and Alpha questions
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
murphytho1401
• 0
1
vote
2
replies
906
views
Different regions for normalisation
DESeq2
median-of-ratios
normalisation
2.6 years ago
msrch
• 0
0
votes
0
replies
1.2k
views
package ‘riboSeqR’ is not available for this version of R
Bioconductor
riboSeqR
2.6 years ago
Javier
• 0
0
votes
2
replies
1.2k
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
2.6 years ago
paria.alipour
• 0
0
votes
1
reply
975
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
2.6 years ago
Grace
• 0
0
votes
2
replies
1.7k
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
2.6 years ago
Yijing
• 0
46,692 results • Page
53 of 934
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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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