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WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
22 minutes ago
w.cookson
• 0
0
votes
0
replies
15
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
4 hours ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
12
views
Materials for liposomes
alabaster.schemas
metaMSdata
7 hours ago
bocsciences
• 0
0
votes
1
reply
24
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 17 hours ago by
James W. MacDonald
65k • written 19 hours ago by
Karen
• 0
0
votes
3
replies
142
views
PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Laura
▴ 10
1
vote
8
replies
251
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 10 hours ago by
Gordon Smyth
50k • written 1 day ago by
Amit
• 0
1
vote
2
replies
101
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 • updated 1 day ago
Mj.A.
• 0
0
votes
2
replies
96
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
2
replies
94
views
From a DNAStringSet to a data.frame
Biostrings
2 days ago
ramiro.barrantes
▴ 10
0
votes
5
replies
115
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Jitendra
▴ 10
0
votes
2
replies
88
views
bioconductor emailing list
Bioconductor
updated 2 days ago by
shepherl
3.8k • written 3 days ago by
1427972815
• 0
2
votes
3
replies
133
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
3
votes
2
replies
113
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
0
votes
0
replies
43
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
3 days ago
gshweta95
• 0
2
votes
1
reply
154
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
1
vote
3
replies
188
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 2 days ago by
alan.ocallaghan
▴ 150 • written 4 days ago by
Najla Abassi
• 0
7
votes
6
replies
322
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
Amit
• 0
0
votes
1
reply
199
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
Gordon
• 0
2
votes
1
reply
116
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
enee
▴ 10
0
votes
0
replies
67
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
5 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
84
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
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
120
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
6 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
0
votes
1
reply
143
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
scoops_streams_06
• 0
1
vote
3
replies
178
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 6 days ago by
Marcel Ramos
690 • written 6 days ago by
Astrid Deschênes
• 0
4
votes
3
replies
358
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 16 hours ago by
Gordon Smyth
50k • written 7 days ago by
Jack S.
▴ 50
0
votes
2
replies
131
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
7 days ago • updated 6 days ago
kcarey
• 0
0
votes
0
replies
64
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
7 days ago
mayra.haedo
• 0
0
votes
0
replies
63
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
7 days ago
taylor.witte
• 0
0
votes
0
replies
79
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
7 days ago
erbrocato
• 0
1
vote
4
replies
182
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
0
votes
2
replies
138
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 8 days ago by
maximilian.beikirch
• 0
0
votes
0
replies
67
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 days ago
BID
• 0
1
vote
3
replies
169
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 12 hours ago by
mercedeh.movassagh
▴ 10 • written 8 days ago by
María
• 0
0
votes
2
replies
134
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 days ago • updated 8 days ago
rocanja
▴ 60
0
votes
2
replies
145
views
Error in msaFun Cannot open input file. No alignment!
msa
written 9 days ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
131
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 9 days ago by
Julie
• 0
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
1
vote
3
replies
221
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 7 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
4
votes
3
replies
161
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 9 days ago by
Georg
• 0
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
2
votes
2
replies
182
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
10 days ago • updated 9 days ago
Eva
▴ 10
0
votes
1
reply
97
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 10 days ago by
Michael Love
41k • written 10 days ago by
rahaf.nazzal9
• 0
0
votes
4
replies
296
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
10 days ago • updated 2 days ago
Efra
• 0
0
votes
1
reply
115
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Yuqin
• 0
1
vote
1
reply
121
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Emma
• 0
4
votes
7
replies
316
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 18 hours ago by
Gordon Smyth
50k • written 11 days ago by
Amit
• 0
1
vote
1
reply
134
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
zoheir.alayash
▴ 10
45,437 results • Page
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Comment: error when using M-values in ChAMP
by
hortenseguillaume96
• 0
Hello Tian, I'd like to get the M-values matrix so that I can carry out a linear regression study. However, when I apply the champ.load fu…
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
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
Answer: error in ChAMP loading file
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