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News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
23 months ago • updated 15 months ago
shepherl
4.3k
4
votes
6
replies
1.9k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
15 months ago
altintas.ali
• 0
2
votes
3
replies
1.3k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
KokiBio
• 0
0
votes
7
replies
1.8k
views
How should I know which platforms are available for TCGA methylation?
TCGAbiolinks
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
xiaofeiwang198266
• 0
1
vote
4
replies
1.2k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
15 months ago
boczniak767
▴ 740
0
votes
0
replies
1.1k
views
News:
Ensembl 113 has been released
ensembl
ensembldb
mart
biomaRt
15 months ago
Ensembl_Jorge
▴ 10
1
vote
9
replies
3.9k
views
Error using champ.import
ChAMP
EPICv2
updated 15 months ago by
Ricky
• 0 • written 2.6 years ago by
medha.suman
• 0
0
votes
1
reply
475
views
enrichKEGG
keggorthology
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
strawberry3
• 0
0
votes
3
replies
1.9k
views
Label specific rows in pheatmap
heatmaps
pheatmap
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Dina
▴ 50
3
votes
4
replies
3.1k
views
News:
Bioconductor 3.20 Release Schedule
software
release
Release
updated 8 months ago by
randyprice13102000
• 0 • written 16 months ago by
shepherl
4.3k
1
vote
2
replies
769
views
edgeR 4.2.2 not compiled for Windows
edger
edgeR
15 months ago
Hongjian
• 0
0
votes
1
reply
411
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
15 months ago
JY
• 0
0
votes
1
reply
499
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
agamemnon
• 0
0
votes
2
replies
538
views
how to extract expression matrix post deseq2
DESeq2
written 15 months ago by
agamemnon
• 0
2
votes
2
replies
1.1k
views
Automatically generate contrasts from a model matrix / formula
limma
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
Jonathan
▴ 10
0
votes
2
replies
573
views
Using Normalized Counts in DESeq2
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
KokiBio
• 0
0
votes
0
replies
377
views
DiffBind subset replicates
DiffBind
15 months ago
Haiping
• 0
1
vote
4
replies
1.2k
views
How to reverse complement some elements of a DNAStringSet
biostr
Biostrings
written 15 months ago by
Christine Jones
• 0
3
votes
2
replies
675
views
When running contrasts, does it use normalized read counts?
DESeq2
15 months ago
Katherine
▴ 20
0
votes
0
replies
547
views
Rsubread - sublong function
pacbio
sublong
Rsubread
15 months ago
thomas.heigl.ibk
• 0
3
votes
4
replies
1.8k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
15 months ago
sukeshinik5
▴ 20
1
vote
3
replies
2.1k
views
featureCounts fails to load annotation file
featurecounts
rnas
RNASeqPower
15 months ago
yasmin.hilliam
▴ 10
0
votes
1
reply
449
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
Bingqian
• 0
1
vote
2
replies
842
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata
Biostrings
updated 13 months ago by
Aidan
▴ 70 • written 15 months ago by
Gerhard Thallinger
▴ 180
3
votes
3
replies
833
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
15 months ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
806
views
Need help interpreting heatmaps from limma
limma
written 15 months ago by
lhwh1208
• 0
0
votes
0
replies
318
views
when FOLD>0, which group of sampls increased?
BASiCS
15 months ago
Jeffcgen2000
• 0
3
votes
4
replies
1.5k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
15 months ago
Eva
▴ 10
1
vote
3
replies
5.7k
views
Unable to install any Bioconductor package with new R 4.4.1 - path nor writable - PLEASE HELP
pathnotwritable
BiocManager
LEA
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
gabry.scata
▴ 10
0
votes
0
replies
320
views
Paired splsda
mixOmics
15 months ago
michelafrancesconi8
• 0
2
votes
1
reply
2.0k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
danphillips28
▴ 10
0
votes
0
replies
703
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
15 months ago
Young Boqin
• 0
0
votes
0
replies
607
views
News:
Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment
SingleCell
15 months ago
info
▴ 10
4
votes
4
replies
870
views
How to conduct maSigPro analysis with only one condition?
maSigPro
masig
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Jiahao Tian
• 0
1
vote
4
replies
1.4k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
Ricardo Iván
• 0
0
votes
1
reply
565
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
Jiahao Tian
• 0
0
votes
0
replies
501
views
DMRcate pcutoff setting
EpicV2
DMRcate
15 months ago
kitzhu
• 0
2
votes
4
replies
1.0k
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
15 months ago
jihoon.kim.1495
▴ 10
0
votes
0
replies
494
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS
alternativesplicing
maser
R
15 months ago
Anke
• 0
0
votes
6
replies
1.5k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 15 months ago by
Michael Love
43k • written 15 months ago by
CriticalPeriod
• 0
1
vote
1
reply
1.0k
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 15 months ago by
Lluís Revilla Sancho
▴ 760 • written 15 months ago by
Nasim
• 0
5
votes
4
replies
1.1k
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
Bioinformagician
• 0
4
votes
1
reply
732
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger
edgeR
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
Hongjian
• 0
2
votes
5
replies
1.1k
views
dmpFinder for other objects
methylset
minfi
dmpFinder
betaHMM
beta
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
neyousha
• 0
0
votes
1
reply
512
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel
ChIPQC
written 15 months ago by
Young Boqin
• 0
0
votes
2
replies
756
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
15 months ago
paul.meraner
• 0
0
votes
0
replies
664
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
15 months ago
info
▴ 10
2
votes
8
replies
2.0k
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 13 months ago by
mercedeh.movassagh
▴ 20 • written 22 months ago by
María Calvo
• 0
1
vote
6
replies
1.6k
views
heatmap with batch effect
DESeq2
BatchEffect
written 15 months ago by
tothuhien
• 0
0
votes
1
reply
596
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi
Annotation
annotation
BiologicalQuestion
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Olajumoke
• 0
46,730 results • Page
15 of 935
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Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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