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0
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replies
162
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
16 days ago
Gimena
• 0
0
votes
2
replies
139
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
16 days ago
Marianna
▴ 20
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 16 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
292
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 8 days ago by
Tim Peters
▴ 170 • written 17 days ago by
s.malik
• 0
1
vote
1
reply
129
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
17 days ago • updated 16 days ago
Layal
• 0
0
votes
2
replies
205
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
22 days ago • updated 17 days ago
w.cookson
• 0
0
votes
2
replies
142
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
17 days ago • updated 16 days ago
michelafrancesconi8
• 0
0
votes
1
reply
111
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Reeya
• 0
0
votes
4
replies
216
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 17 days ago by
Michael Love
41k • written 17 days ago by
Aidan
• 0
0
votes
4
replies
385
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
18 days ago • updated 17 days ago
Lucy
▴ 60
0
votes
1
reply
91
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
Leyre
• 0
0
votes
2
replies
156
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
18 days ago • updated 17 days ago
Seongsu
• 0
0
votes
2
replies
157
views
Gene Ontology doubt
microbiomeExplorer
19 days ago • updated 15 days ago
Bhawna
• 0
0
votes
1
reply
147
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 18 days ago by
Michael Love
41k • written 21 days ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
128
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
ja569116
• 0
0
votes
2
replies
261
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
19 days ago • updated 14 days ago
fer_talavera
• 0
0
votes
2
replies
212
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
19 days ago • updated 6 hours ago
isaac.vock
• 0
0
votes
7
replies
321
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
20 days ago • updated 17 days ago
needNGS
• 0
14
votes
20
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 2 minutes ago
Chris
• 0
3
votes
5
replies
327
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 19 days ago by
Gordon Smyth
50k • written 22 days ago by
Fabian
• 0
0
votes
2
replies
154
views
Minfi - estimatecellscount
min
minfi
21 days ago
clacarion
• 0
0
votes
0
replies
93
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 days ago
feather-W
• 0
0
votes
0
replies
91
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 days ago
Ankit
▴ 20
0
votes
6
replies
304
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 21 days ago by
Gordon Smyth
50k • written 22 days ago by
Faisal
• 0
1
vote
5
replies
288
views
fgsea fork
fgsea
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
yimjohns
• 0
0
votes
1
reply
134
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Mikushi
• 0
0
votes
0
replies
78
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
22 days ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
474
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 22 days ago by
Gordon Smyth
50k • written 24 days ago by
Amit
• 0
0
votes
1
reply
109
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Karen
• 0
2
votes
3
replies
314
views
PCA of different bacterial species
DESeq2
updated 23 days ago by
Michael Love
41k • written 23 days ago by
Laura
▴ 10
1
vote
2
replies
208
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
24 days ago
Mj.A.
• 0
0
votes
1
reply
226
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
6 weeks ago • updated 24 days ago
shepherl
3.8k
0
votes
2
replies
182
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 24 days ago by
Michael Love
41k • written 24 days ago by
SG
• 0
2
votes
3
replies
224
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 24 days ago by
Wei Shi
★ 3.6k • written 25 days ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
190
views
From a DNAStringSet to a data.frame
Biostrings
24 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
148
views
collapseReplicates dimension error
DESeq2
Dese
updated 24 days ago by
Michael Love
41k • written 28 days ago by
Léa
• 0
5
votes
25
replies
785
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 14 days ago by
Gordon Smyth
50k • written 25 days ago by
Jitendra
▴ 10
0
votes
2
replies
152
views
bioconductor emailing list
Bioconductor
updated 25 days ago by
shepherl
3.8k • written 25 days ago by
1427972815
• 0
3
votes
2
replies
190
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
25 days ago
Anita
▴ 10
3
votes
3
replies
334
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 25 days ago by
alan.ocallaghan
▴ 160 • written 26 days ago by
Najla Abassi
• 0
2
votes
1
reply
209
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 25 days ago by
ATpoint
★ 4.0k • written 25 days ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
98
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
25 days ago
gshweta95
• 0
0
votes
2
replies
307
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
28 days ago • updated 16 days ago
Gordon
• 0
7
votes
6
replies
410
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 27 days ago by
Gordon Smyth
50k • written 28 days ago by
Amit
• 0
2
votes
1
reply
176
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 28 days ago by
enee
▴ 10
0
votes
0
replies
117
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
28 days ago
Maria Doyle
▴ 70
0
votes
0
replies
107
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
28 days ago
shepherl
3.8k
0
votes
1
reply
205
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
scoops_streams_06
• 0
0
votes
0
replies
99
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
28 days ago
nromerov
• 0
1
vote
2
replies
198
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
29 days ago • updated 23 days ago
Chanderkant Chaudhary
• 0
45,551 results • Page
3 of 912
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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