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PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
1 minute ago • updated just now
Ankit
▴ 20
0
votes
3
replies
61
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 1 minute ago by
Michael Love
41k • written 15 hours ago by
Faisal
• 0
0
votes
1
reply
51
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 44 minutes ago by
Gordon Smyth
50k • written 14 hours ago by
Fabian
• 0
0
votes
1
reply
19
views
fgsea fork
fgsea
updated 6 minutes ago by
shepherl
3.8k • written 8 hours ago by
yimjohns
• 0
0
votes
1
reply
41
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 14 hours ago by
Michael Love
41k • written 15 hours ago by
Mikushi
• 0
0
votes
1
reply
54
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
updated 20 hours ago by
James W. MacDonald
65k • written 20 hours ago by
w.cookson
• 0
0
votes
0
replies
24
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
1 day ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
24
views
Materials for liposomes
alabaster.schemas
metaMSdata
1 day ago
bocsciences
• 0
1
vote
8
replies
285
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
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
115
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 3 days ago by
Wei Shi
★ 3.6k • written 3 days ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
112
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 7 days ago by
Léa
• 0
0
votes
5
replies
130
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
Jitendra
▴ 10
0
votes
2
replies
100
views
bioconductor emailing list
Bioconductor
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
1427972815
• 0
3
votes
2
replies
124
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
199
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
159
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 4 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
4 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
335
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
124
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
152
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
141
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
185
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
507
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
69
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
187
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
9 days ago • updated 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
183
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
189
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 1 day ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
0
votes
2
replies
139
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
222
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
139
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
45,442 results • Page
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Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
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
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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