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0
votes
2
replies
159
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
4 weeks ago • updated 29 days ago
Marianna
▴ 20
0
votes
2
replies
184
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
4 weeks ago • updated 29 days ago
Gimena
• 0
0
votes
6
replies
330
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 22 days ago by
Tim Peters
▴ 170 • written 4 weeks ago by
s.malik
• 0
1
vote
10
replies
445
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 24 days ago
Kurtis
• 0
1
vote
1
reply
150
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago
Layal
• 0
0
votes
2
replies
169
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago
michelafrancesconi8
• 0
0
votes
1
reply
141
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Reeya
• 0
0
votes
4
replies
255
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
1
reply
108
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Leyre
• 0
0
votes
4
replies
416
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago
Lucy
▴ 60
0
votes
2
replies
180
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
4 weeks ago
Seongsu
• 0
0
votes
1
reply
156
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
ja569116
• 0
0
votes
2
replies
175
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 28 days ago
Bhawna
• 0
0
votes
2
replies
294
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 27 days ago
fer_talavera
• 0
1
vote
2
replies
225
views
MethylKit read issue
methylKit
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
0
votes
2
replies
253
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
7
replies
389
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
4 weeks ago
needNGS
• 0
0
votes
1
reply
169
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
saadmurtazakhan
▴ 10
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
0
votes
4
replies
238
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
0
votes
0
replies
109
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 weeks ago
Ankit
▴ 20
1
vote
5
replies
335
views
fgsea fork
fgsea
updated 4 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
yimjohns
• 0
3
votes
5
replies
372
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Fabian
• 0
0
votes
6
replies
349
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Faisal
• 0
0
votes
1
reply
159
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Mikushi
• 0
0
votes
2
replies
228
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
5 weeks ago • updated 4 weeks ago
w.cookson
• 0
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
1
reply
136
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Karen
• 0
2
votes
3
replies
346
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Laura
▴ 10
2
votes
8
replies
520
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
1
vote
2
replies
228
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
5 weeks ago
Mj.A.
• 0
0
votes
2
replies
205
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
SG
• 0
2
votes
2
replies
220
views
From a DNAStringSet to a data.frame
Biostrings
5 weeks ago
ramiro.barrantes
▴ 10
5
votes
25
replies
884
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
174
views
bioconductor emailing list
Bioconductor
updated 5 weeks ago by
shepherl
3.9k • written 5 weeks ago by
1427972815
• 0
2
votes
3
replies
253
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 5 weeks ago by
Wei Shi
★ 3.6k • written 5 weeks ago by
thomas.heigl.ibk
• 0
3
votes
2
replies
212
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
5 weeks ago
Anita
▴ 10
0
votes
0
replies
117
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
5 weeks ago
gshweta95
• 0
2
votes
1
reply
231
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
390
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 weeks ago by
Najla Abassi
• 0
7
votes
6
replies
449
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
0
votes
2
replies
351
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 4 weeks ago
Gordon
• 0
2
votes
1
reply
209
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
0
votes
0
replies
140
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
5 weeks ago
Maria Doyle
▴ 70
1
vote
0
replies
177
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
5 weeks ago
shepherl
3.9k
0
votes
1
reply
169
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 6 weeks ago by
Léa
• 0
0
votes
0
replies
115
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
6 weeks ago
nromerov
• 0
1
vote
2
replies
229
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
6 weeks ago • updated 5 weeks ago
Chanderkant Chaudhary
• 0
0
votes
1
reply
232
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
scoops_streams_06
• 0
45,611 results • Page
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Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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