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2
votes
12
replies
2.9k
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limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
15 months ago • updated 14 months ago
john
• 0
0
votes
2
replies
1.0k
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 15 months ago by
Aleksandra
• 0
1
vote
3
replies
1.4k
views
Tutorial regarding metabolomics with R
Bioconductor
Metabolomics
xcms
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
abhisek001
• 0
1
vote
1
reply
736
views
DataFrame Character Truncation
S4Vectors
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Dario Strbenac
★ 1.6k
4
votes
6
replies
2.0k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
abadgerw
• 0
5
votes
13
replies
2.6k
views
Installing annotation package in locally
AnnotationDbi
AnnotationHub
Annotation
AnnotationForge
15 months ago
KABILAN
• 0
0
votes
2
replies
1.1k
views
DiffBind dba.report discrepancy
DiffBind
15 months ago
aelbassiouny
• 0
1
vote
8
replies
1.7k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea
mice
org.Mm.eg.db
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Gordon
• 0
0
votes
1
reply
519
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
nicolettacommins
• 0
0
votes
2
replies
1.5k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
15 months ago
José
• 0
0
votes
0
replies
438
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment
SingleCellExperiment
15 months ago
Ibrahim
• 0
0
votes
1
reply
895
views
MethylKit CpG Island annotation for Hg38
methylKit
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Satyanarayan
• 0
0
votes
5
replies
1.2k
views
Need help converting vcf files to snp
VCFArray
15 months ago
patrice.bridges457
• 0
0
votes
11
replies
2.9k
views
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
2.0k
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
1.4k
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
480
views
enrichKEGG
keggorthology
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
strawberry3
• 0
0
votes
3
replies
2.0k
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
3.2k
views
News:
Bioconductor 3.20 Release Schedule
software
release
Release
updated 9 months ago by
randyprice13102000
• 0 • written 17 months ago by
shepherl
4.3k
1
vote
2
replies
782
views
edgeR 4.2.2 not compiled for Windows
edger
edgeR
15 months ago
Hongjian
• 0
0
votes
1
reply
413
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
503
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
543
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
576
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
382
views
DiffBind subset replicates
DiffBind
15 months ago
Haiping
• 0
1
vote
4
replies
1.3k
views
How to reverse complement some elements of a DNAStringSet
biostr
Biostrings
written 15 months ago by
Christine Jones
• 0
3
votes
2
replies
695
views
When running contrasts, does it use normalized read counts?
DESeq2
15 months ago
Katherine
▴ 20
0
votes
0
replies
574
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
2.3k
views
featureCounts fails to load annotation file
featurecounts
rnas
RNASeqPower
15 months ago
yasmin.hilliam
▴ 10
0
votes
1
reply
452
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
855
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
842
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
15 months ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
817
views
Need help interpreting heatmaps from limma
limma
written 15 months ago by
lhwh1208
• 0
0
votes
0
replies
321
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
6.0k
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 16 months ago by
gabry.scata
▴ 10
0
votes
0
replies
323
views
Paired splsda
mixOmics
16 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 16 months ago by
James W. MacDonald
68k • written 16 months ago by
danphillips28
▴ 10
0
votes
0
replies
717
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
16 months ago
Young Boqin
• 0
0
votes
0
replies
619
views
News:
Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment
SingleCell
16 months ago
info
▴ 10
4
votes
4
replies
878
views
How to conduct maSigPro analysis with only one condition?
maSigPro
masig
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
Jiahao Tian
• 0
1
vote
4
replies
1.5k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 15 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Ricardo Iván
• 0
0
votes
1
reply
566
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 16 months ago by
Michael Love
43k • written 16 months ago by
Jiahao Tian
• 0
0
votes
0
replies
513
views
DMRcate pcutoff setting
EpicV2
DMRcate
16 months ago
kitzhu
• 0
46,739 results • Page
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Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Answer: Confused about the CPM and TMM normalization in edgeR
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
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