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fgsea fork
fgsea
6 hours ago
yimjohns
• 0
0
votes
0
replies
37
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
12 hours ago
Fabian
• 0
0
votes
1
reply
40
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 12 hours ago by
Michael Love
41k • written 13 hours ago by
Mikushi
• 0
0
votes
1
reply
50
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
13 hours ago • updated 12 hours ago
Faisal
• 0
0
votes
1
reply
53
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
updated 18 hours ago by
James W. MacDonald
65k • written 18 hours ago by
w.cookson
• 0
0
votes
0
replies
24
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
23 hours ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
23
views
Materials for liposomes
alabaster.schemas
metaMSdata
1 day ago
bocsciences
• 0
1
vote
8
replies
283
views
Microarray Limma Model fitting and DEG
limma
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updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
Amit
• 0
0
votes
1
reply
43
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
3
replies
166
views
PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Laura
▴ 10
1
vote
2
replies
114
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
147
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
23 days ago • updated 2 days ago
shepherl
3.8k
0
votes
2
replies
104
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 2 days ago by
Michael Love
41k • written 3 days ago by
SG
• 0
2
votes
3
replies
143
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
111
views
From a DNAStringSet to a data.frame
Biostrings
3 days ago • updated 2 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
90
views
collapseReplicates dimension error
DESeq2
Dese
updated 3 days ago by
Michael Love
41k • written 6 days ago by
Léa
• 0
0
votes
5
replies
129
views
limma models out of memory issue on Slurm HPC
Regression
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updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Jitendra
▴ 10
0
votes
2
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99
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bioconductor emailing list
Bioconductor
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
1427972815
• 0
3
votes
2
replies
123
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
1
vote
3
replies
198
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Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
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updated 3 days ago by
alan.ocallaghan
▴ 150 • written 4 days ago by
Najla Abassi
• 0
2
votes
1
reply
159
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
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scater
scuttle
updated 3 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
47
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
3 days ago
gshweta95
• 0
0
votes
1
reply
204
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
333
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
Amit
• 0
2
votes
1
reply
123
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
71
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
6 days ago
Maria Doyle
▴ 70
0
votes
0
replies
51
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 days ago
shepherl
3.8k
0
votes
1
reply
151
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
scoops_streams_06
• 0
0
votes
0
replies
57
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
7 days ago
nromerov
• 0
1
vote
2
replies
140
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
184
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 7 days ago by
Marcel Ramos
690 • written 7 days ago by
Astrid Deschênes
• 0
4
votes
3
replies
476
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 1 day ago by
Gordon Smyth
50k • written 8 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 8 days ago by
jandrade
• 0 • written 6.3 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
137
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 days ago • updated 7 days ago
kcarey
• 0
0
votes
0
replies
68
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
8 days ago
mayra.haedo
• 0
0
votes
0
replies
64
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
8 days ago
taylor.witte
• 0
0
votes
0
replies
81
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 days ago
erbrocato
• 0
1
vote
4
replies
186
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 days ago
samuel.channon
• 0
1
vote
3
replies
227
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 8 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
181
views
Help with Complex DESeq2 Design
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
kelsey.beavers
• 0
0
votes
2
replies
142
views
Visium RNA
metaMSdata
updated 9 days ago by
vvvc360work2
• 0 • written 9 days ago by
Karlison
• 0
1
vote
2
replies
162
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 9 days ago by
ATpoint
★ 4.0k • written 9 days ago by
maximilian.beikirch
• 0
0
votes
0
replies
72
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
9 days ago
BID
• 0
1
vote
3
replies
188
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 1 day ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
0
votes
2
replies
138
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
10 days ago • updated 9 days ago
rocanja
▴ 60
1
vote
3
replies
3.0k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 10 days ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
0
votes
2
replies
147
views
Error in msaFun Cannot open input file. No alignment!
msa
written 10 days ago by
Kamil Slowikowski
▴ 30
2
votes
3
replies
220
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
0
votes
1
reply
137
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 10 days ago by
Julie
• 0
4
votes
3
replies
167
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 10 days ago by
Georg
• 0
193 results • Page
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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
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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