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Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 2 days ago by
Mj.A.
• 0 • written 5.2 years ago by
shepherl
3.8k
11
votes
4
replies
7.2k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 1 day ago by
Peter Langfelder
★ 2.9k • written 9.0 years ago by
brohawndg
▴ 150
0
votes
3
replies
2.2k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm
LEA
updated 4 days ago by
m.charters
• 0 • written 2.9 years ago by
valentinarov
• 0
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 7 hours ago by
hortenseguillaume96
• 0 • written 6.2 years ago by
a.mcneill
• 0
0
votes
1
reply
559
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
0
votes
2
replies
523
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 3 days ago by
CHEN
• 0 • written 10 months ago by
Saanchi
• 0
4
votes
3
replies
401
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 23 hours ago by
Gordon Smyth
50k • written 7 days ago by
Jack S.
▴ 50
0
votes
7
replies
339
views
DESeq2 filtering vs edgeR filtering
DESeq2
15 days ago • updated 2 days ago
fr8712ca-s
• 0
7
votes
6
replies
326
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Amit
• 0
4
votes
7
replies
324
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 1 day ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
0
votes
6
replies
324
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
21 days ago • updated 2 days ago
Lily Cheang
• 0
0
votes
4
replies
302
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
10 days ago • updated 2 days ago
Efra
• 0
1
vote
8
replies
271
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 18 hours ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
0
votes
1
reply
201
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
1
vote
3
replies
193
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
1
vote
1
reply
189
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 2 days ago by
SamGG
▴ 330 • written 5 weeks ago by
jarod
▴ 30
1
vote
3
replies
181
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
1
vote
3
replies
177
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 19 hours ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
0
votes
3
replies
158
views
PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Laura
▴ 10
2
votes
1
reply
156
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 3 days ago by
ATpoint
★ 4.0k • written 3 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
146
views
Error in msaFun Cannot open input file. No alignment!
msa
written 9 days ago by
Kamil Slowikowski
▴ 30
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
1
reply
144
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
23 days ago • updated 2 days ago
shepherl
3.8k
2
votes
3
replies
137
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
0
votes
1
reply
135
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
1
vote
2
replies
131
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
0
votes
5
replies
122
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Jitendra
▴ 10
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
3
votes
2
replies
117
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
1
vote
2
replies
106
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
2
votes
2
replies
100
views
From a DNAStringSet to a data.frame
Biostrings
2 days ago
ramiro.barrantes
▴ 10
0
votes
2
replies
99
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
0
votes
2
replies
91
views
bioconductor emailing list
Bioconductor
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
1427972815
• 0
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
0
replies
68
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
6 days ago
Maria Doyle
▴ 70
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
0
votes
0
replies
50
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 days ago
shepherl
3.8k
0
votes
0
replies
44
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
3 days ago
gshweta95
• 0
0
votes
1
reply
41
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
updated 6 hours ago by
James W. MacDonald
65k • written 7 hours ago by
w.cookson
• 0
0
votes
1
reply
35
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Karen
• 0
0
votes
1
reply
24
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
1 hour ago
Faisal
• 0
0
votes
1
reply
21
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 1 hour ago by
Michael Love
41k • written 2 hours ago by
Mikushi
• 0
0
votes
0
replies
20
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
11 hours ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
17
views
Materials for liposomes
alabaster.schemas
metaMSdata
14 hours ago
bocsciences
• 0
0
votes
0
replies
13
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
1 hour ago
Fabian
• 0
45 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
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…
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
Awards
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James W. MacDonald
65k
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50k
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