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0
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2
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770
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
21 months ago
michelafrancesconi8
• 0
0
votes
1
reply
885
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Reeya
• 0
0
votes
4
replies
1.1k
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Aidan
• 0
0
votes
4
replies
1.5k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
21 months ago
Lucy
▴ 60
0
votes
1
reply
687
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Leyre
• 0
0
votes
2
replies
1.1k
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
21 months ago
Seongsu
• 0
0
votes
2
replies
913
views
Gene Ontology doubt
microbiomeExplorer
21 months ago
Bhawna
• 0
0
votes
1
reply
847
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 21 months ago by
Michael Love
43k • written 21 months ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
969
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
ja569116
• 0
0
votes
2
replies
854
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
21 months ago
fer_talavera
• 0
0
votes
7
replies
2.4k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
21 months ago
needNGS
• 0
15
votes
23
replies
5.4k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 months ago • updated 20 months ago
Chris
▴ 20
3
votes
6
replies
2.3k
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
written 21 months ago by
Fabian
• 0
0
votes
4
replies
1.1k
views
Minfi - estimatecellscount
min
minfi
updated 20 months ago by
James W. MacDonald
68k • written 21 months ago by
clacarion
• 0
0
votes
0
replies
663
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 months ago
feather-W
• 0
0
votes
0
replies
654
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 months ago
Ankit
▴ 20
0
votes
6
replies
1.4k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Faisal
• 0
1
vote
5
replies
1.3k
views
fgsea fork
fgsea
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
yimjohns
• 0
0
votes
1
reply
453
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Mikushi
• 0
0
votes
0
replies
643
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 months ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
1.5k
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Amit
• 0
0
votes
1
reply
710
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Karen
• 0
2
votes
4
replies
1.4k
views
PCA of different bacterial species
DESeq2
written 21 months ago by
Laura
▴ 10
1
vote
2
replies
790
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
21 months ago
Mj.A.
▴ 20
0
votes
1
reply
1.7k
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
22 months ago • updated 21 months ago
shepherl
4.2k
0
votes
2
replies
1.1k
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 21 months ago by
Michael Love
43k • written 21 months ago by
SG
• 0
2
votes
3
replies
1.1k
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 21 months ago by
Wei Shi
★ 3.6k • written 21 months ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
2.4k
views
From a DNAStringSet to a data.frame
Biostrings
21 months ago
ramiro.barrantes
▴ 10
0
votes
1
reply
617
views
collapseReplicates dimension error
DESeq2
Dese
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Léa
• 0
5
votes
25
replies
3.2k
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Jitendra
▴ 10
2
votes
4
replies
917
views
bioconductor emailing list
Bioconductor
21 months ago • updated 16 months ago
XFWu
• 0
3
votes
2
replies
808
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
21 months ago
Anita
▴ 10
3
votes
3
replies
2.4k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 21 months ago by
alan.ocallaghan
▴ 160 • written 21 months ago by
Najla Abassi
• 0
2
votes
1
reply
1.0k
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Dario Strbenac
★ 1.6k
0
votes
0
replies
810
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
21 months ago
gshweta95
• 0
0
votes
2
replies
2.0k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
21 months ago
Gordon
• 0
7
votes
6
replies
1.3k
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Amit
• 0
2
votes
2
replies
1.5k
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 21 months ago by
enee
▴ 10
0
votes
1
reply
1.2k
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
updated 6 months ago by
Ray
• 0 • written 21 months ago by
Maria Doyle
▴ 110
0
votes
1
reply
1.1k
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
scoops_streams_06
• 0
0
votes
0
replies
499
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
21 months ago
nromerov
• 0
1
vote
2
replies
906
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
21 months ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
838
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 21 months ago by
Marcel Ramos
700 • written 21 months ago by
Astrid Deschênes
• 0
8
votes
5
replies
3.5k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 14 months ago by
Gordon Smyth
53k • written 21 months ago by
Jack S.
▴ 60
4
votes
4
replies
5.3k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 21 months ago by
jandrade
• 0 • written 8.0 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
2.1k
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
21 months ago
kcarey
• 0
0
votes
0
replies
721
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
21 months ago
mayra.haedo
• 0
0
votes
0
replies
602
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
21 months ago
erbrocato
• 0
1
vote
4
replies
1.2k
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
21 months ago
samuel.channon
• 0
2
votes
3
replies
873
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
andrebolerbarros
▴ 20
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