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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
1 hour ago
dudutchy
• 0
0
votes
1
reply
132
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 11 hours ago by
James W. MacDonald
68k • written 1 day ago by
sk
• 0
0
votes
0
replies
24
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
12 hours ago
Muhammad
• 0
0
votes
0
replies
18
views
How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
13 hours ago
Charles
• 0
0
votes
0
replies
9
views
Spam:
County Group Wave City Ghaziabad
ri16cod.db
ncdfFlow
15 hours ago
countywavecityghaziabad
0
1
vote
5
replies
731
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 11 hours ago by
James W. MacDonald
68k • written 1 day ago by
caroline.zanchi
• 0
0
votes
0
replies
39
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
1 day ago
s.malik
• 0
0
votes
1
reply
176
views
Error in readCodelinkSet function
error
codelink
updated 1 day ago by
James W. MacDonald
68k • written 1 day ago by
nazaninhoseinkhan
• 0
0
votes
0
replies
59
views
Combat-seq usage
sva
updated 1 day ago by
ATpoint
★ 4.8k • written 1 day ago by
bbao
▴ 10
0
votes
1
reply
167
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 1 day ago by
ATpoint
★ 4.8k • written 2 days ago by
yob4003
• 0
0
votes
1
reply
143
views
What happened to the Joost2016 dataset
org.Sc.sgd.db
updated 1 day ago by
shepherl
4.1k • written 3 days ago by
clementleong
• 0
2
votes
5
replies
847
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 7 days ago by
Thomas
• 0
0
votes
3
replies
50k
views
SingleR Label.Ont
SingleR
written 20 months ago by
saeed.khalili
• 0
0
votes
1
reply
335
views
News:
Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt
ensembldb
updated 4 days ago by
sophisticated.blackbird.meau
• 0 • written 6 days ago by
Aleena_Ensembl
▴ 30
5
votes
7
replies
2.7k
views
limma correction for tumor purity
limma
7 days ago • updated 1 day ago
gabriella.jacobson-eisenberg
▴ 20
0
votes
1
reply
235
views
Filtering out non-variable probes from EPICv2 matrix
DMRcate
EPICv2manifest
updated 7 days ago by
James W. MacDonald
68k • written 11 days ago by
Sasha
• 0
0
votes
1
reply
128
views
FlowSOM is unable to create Output
FlowSOM
updated 7 days ago by
ATpoint
★ 4.8k • written 7 days ago by
marco.klein1
• 0
8
votes
3
replies
2.3k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 5 days ago by
Michael Love
43k • written 8 days ago by
Cassia
▴ 40
2
votes
14
replies
2.5k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
8 days ago • updated 3 days ago
petergrahamclark
• 0
0
votes
5
replies
477
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
written 8 weeks ago by
Wolfgang RAFFELSBERGER
▴ 140
0
votes
4
replies
1.0k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 7 weeks ago by
Alex
• 0
1
vote
7
replies
3.3k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 8 days ago by
QFC
• 0 • written 2.1 years ago by
Oscar
▴ 10
2
votes
3
replies
1.3k
views
Filtering after DESeq
DESeq2
IHW
updated 8 days ago by
ChaseWendrix
• 0 • written 18 days ago by
caroline.zanchi
• 0
0
votes
4
replies
926
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
9 days ago • updated 3 days ago
sk
• 0
0
votes
3
replies
674
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR
limma
written 5 weeks ago by
skiaphrene
▴ 10
1
vote
5
replies
824
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
updated 8 days ago by
Gordon Smyth
52k • written 11 days ago by
caroline.zanchi
• 0
0
votes
2
replies
646
views
Version conflict when pushing to scQTLtools devel branch
Bioconductor
written 27 days ago by
XFWu
• 0
2
votes
5
replies
1.5k
views
Unable to install a forged BSgenome package
BSgenomeForge
updated 8 days ago by
James W. MacDonald
68k • written 11 days ago by
JABEZ RAJU
• 0
1
vote
2
replies
1.1k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
updated 12 days ago by
James W. MacDonald
68k • written 13 days ago by
Franz Bachmann
• 0
0
votes
3
replies
606
views
Discrepancies in normalised count data vs unnormalised
DESeq2
updated 8 days ago by
swbarnes2
★ 1.4k • written 13 days ago by
AMgroup
• 0
0
votes
2
replies
470
views
Design formula for circadian time-course data for vst() function
DESeq2
14 days ago
Vishnu
• 0
0
votes
4
replies
513
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
updated 7 days ago by
Gordon Smyth
52k • written 16 days ago by
massimo
• 0
0
votes
0
replies
236
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
17 days ago
jamiecatalano2
• 0
1
vote
3
replies
995
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 18 days ago by
James W. MacDonald
68k • written 20 days ago by
Carolina
• 0
0
votes
1
reply
257
views
RNA-seq input to GRaNIE
GRaNIE
updated 19 days ago by
James W. MacDonald
68k • written 19 days ago by
maia.malonzo
• 0
0
votes
1
reply
501
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
updated 19 days ago by
sergisayolspuig
▴ 80 • written 6 months ago by
daccar98
• 0
0
votes
2
replies
591
views
Analyzing TnSeq data with DESeq2
DESeq2
written 20 days ago by
newfunland
• 0
1
vote
5
replies
1.5k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
written 6 weeks ago by
slizchap
• 0
0
votes
1
reply
595
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
updated 12 days ago by
James W. MacDonald
68k • written 20 days ago by
Kateřina
• 0
0
votes
6
replies
1.7k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
written 15 months ago by
Maria Doyle
▴ 100
2
votes
1
reply
444
views
ROAST for small sets
limma
mroast
updated 20 days ago by
Gordon Smyth
52k • written 21 days ago by
Jay
• 0
0
votes
1
reply
895
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
updated 21 days ago by
Michael Love
43k • written 7 weeks ago by
Simran
• 0
0
votes
2
replies
499
views
Differing results with DESeq2
DESeq2
updated 19 days ago by
JKim
• 0 • written 5 weeks ago by
hampsdiv
• 0
0
votes
1
reply
106
views
Make DEXSeq plot normal scale
DEXSeq
Dexseq
updated 21 days ago by
James W. MacDonald
68k • written 22 days ago by
Rico
• 0
0
votes
2
replies
366
views
RNA Seq using Lrt
DESeq2
21 days ago • updated 20 days ago
Rob
• 0
10
votes
13
replies
1.8k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 20 days ago by
Gordon Smyth
52k • written 22 days ago by
Kinnary
▴ 20
0
votes
3
replies
962
views
Gene Ontology (GO) Analysis
GOstats
hyperGTest
GO
enrichGO
clusterProfiler
23 days ago • updated 3 days ago
GA
▴ 10
0
votes
0
replies
105
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
23 days ago
Shaimaa Gamal
• 0
5
votes
10
replies
2.1k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
written 5 months ago by
chris2.a.white
• 0
0
votes
0
replies
80
views
GRaNIE with no internet
GRaNIE
26 days ago
maia.malonzo
• 0
46,493 results • Page
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Recent ...
Replies
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
by
James W. MacDonald
68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Comment: Heatmap of a transformed deseq object with pheatmap
by
James W. MacDonald
68k
The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…
Answer: Heatmap of a transformed deseq object with pheatmap
by
James W. MacDonald
68k
Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
It is in ! It just took longer than planned :) ... aaaand now that I added the heatmap in I realize lits of genes really do not look like t…
Votes
Comment: Heatmap of a transformed deseq object with pheatmap
DESeq2: Question about the alpha in summary() and results()
Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
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