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Doing comparison of RNA-seq data using Deseq2
DESeq2
metaMSdata
1 minute ago
Faisal
• 0
0
votes
0
replies
2
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
13 minutes ago • updated 10 minutes ago
Mikushi
• 0
0
votes
1
reply
37
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
updated 4 hours ago by
James W. MacDonald
65k • written 5 hours ago by
w.cookson
• 0
0
votes
0
replies
20
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
9 hours ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
16
views
Materials for liposomes
alabaster.schemas
metaMSdata
12 hours ago
bocsciences
• 0
1
vote
8
replies
267
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 16 hours ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
0
votes
1
reply
32
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 23 hours ago by
James W. MacDonald
65k • written 1 day ago by
Karen
• 0
0
votes
3
replies
152
views
PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Laura
▴ 10
1
vote
2
replies
104
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
2 days ago
Mj.A.
• 0
0
votes
1
reply
143
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
23 days ago • updated 2 days ago
shepherl
3.8k
0
votes
2
replies
97
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 2 days ago by
Michael Love
41k • written 2 days ago by
SG
• 0
2
votes
3
replies
135
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 2 days ago by
Wei Shi
★ 3.6k • written 3 days ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
99
views
From a DNAStringSet to a data.frame
Biostrings
2 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
87
views
collapseReplicates dimension error
DESeq2
Dese
updated 2 days ago by
Michael Love
41k • written 6 days ago by
Léa
• 0
0
votes
5
replies
118
views
limma models out of memory issue on Slurm HPC
Regression
limma
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HPC
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Jitendra
▴ 10
0
votes
2
replies
90
views
bioconductor emailing list
Bioconductor
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
1427972815
• 0
3
votes
2
replies
116
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
1
vote
3
replies
192
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 3 days ago by
alan.ocallaghan
▴ 150 • written 4 days ago by
Najla Abassi
• 0
2
votes
1
reply
155
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
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updated 3 days ago by
ATpoint
★ 4.0k • written 3 days ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
43
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
3 days ago
gshweta95
• 0
0
votes
1
reply
200
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
Gordon
• 0
7
votes
6
replies
325
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Amit
• 0
2
votes
1
reply
117
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
enee
▴ 10
0
votes
0
replies
67
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
6 days ago
Maria Doyle
▴ 70
0
votes
0
replies
50
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 days ago
shepherl
3.8k
0
votes
1
reply
145
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
scoops_streams_06
• 0
0
votes
0
replies
55
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
6 days ago
nromerov
• 0
1
vote
2
replies
128
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
180
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 6 days ago by
Marcel Ramos
690 • written 7 days ago by
Astrid Deschênes
• 0
4
votes
3
replies
390
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 21 hours ago by
Gordon Smyth
50k • written 7 days ago by
Jack S.
▴ 50
4
votes
4
replies
3.6k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 7 days ago by
jandrade
• 0 • written 6.3 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
133
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 days ago • updated 7 days ago
kcarey
• 0
0
votes
0
replies
66
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
8 days ago
mayra.haedo
• 0
0
votes
0
replies
63
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
8 days ago
taylor.witte
• 0
0
votes
0
replies
79
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 days ago
erbrocato
• 0
1
vote
4
replies
184
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 days ago • updated 7 days ago
samuel.channon
• 0
1
vote
3
replies
222
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 7 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
177
views
Help with Complex DESeq2 Design
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
kelsey.beavers
• 0
0
votes
2
replies
141
views
Visium RNA
metaMSdata
updated 8 days ago by
vvvc360work2
• 0 • written 8 days ago by
Karlison
• 0
1
vote
2
replies
158
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
maximilian.beikirch
• 0
0
votes
0
replies
68
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
9 days ago
BID
• 0
1
vote
3
replies
173
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 17 hours ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
0
votes
2
replies
135
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 days ago • updated 8 days ago
rocanja
▴ 60
1
vote
3
replies
2.9k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 9 days ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
0
votes
2
replies
145
views
Error in msaFun Cannot open input file. No alignment!
msa
written 9 days ago by
Kamil Slowikowski
▴ 30
2
votes
3
replies
217
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
0
votes
1
reply
134
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 9 days ago by
Julie
• 0
4
votes
3
replies
163
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 10 days ago by
Georg
• 0
3
votes
15
replies
2.6k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 10 days ago
shepherl
3.8k
2
votes
2
replies
184
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
10 days ago
Eva
▴ 10
45,438 results • Page
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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