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0
replies
14
views
Can't install BioC packages (and manager) behind firewall
Install
3 hours ago
delphine
• 0
2
votes
3
replies
222
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub
HubPub
ExperimentHub
updated 2 days ago by
James W. MacDonald
68k • written 2 days ago by
igor
▴ 50
4
votes
2
replies
562
views
GAlignments Cigar to GRanges
GenomicRanges
cigarRangesAlongReferenceSpace
GenomicAlignments
Cigar
2 days ago • updated 1 day ago
pineiroalejandro
▴ 10
0
votes
0
replies
58
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
2 days ago
dudutchy
• 0
0
votes
0
replies
40
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
3 days ago
Muhammad
• 0
0
votes
2
replies
298
views
How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 1 day ago by
Hervé Pagès
16k • written 3 days ago by
Charles
• 0
0
votes
0
replies
10
views
Spam:
County Group Wave City Ghaziabad
ri16cod.db
ncdfFlow
3 days ago
countywavecityghaziabad
0
3
votes
1
reply
319
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 3 days ago by
James W. MacDonald
68k • written 3 days ago by
sk
• 0
1
vote
5
replies
960
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 3 days ago by
James W. MacDonald
68k • written 3 days ago by
caroline.zanchi
▴ 10
0
votes
0
replies
48
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
4 days ago
s.malik
• 0
0
votes
1
reply
197
views
Error in readCodelinkSet function
error
codelink
updated 4 days ago by
James W. MacDonald
68k • written 4 days ago by
nazaninhoseinkhan
• 0
0
votes
0
replies
80
views
Combat-seq usage
sva
updated 4 days ago by
ATpoint
★ 4.8k • written 4 days ago by
bbao
▴ 10
0
votes
1
reply
188
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 4 days ago by
ATpoint
★ 4.8k • written 5 days ago by
yob4003
• 0
0
votes
1
reply
159
views
What happened to the Joost2016 dataset
org.Sc.sgd.db
updated 4 days ago by
shepherl
4.1k • written 6 days ago by
clementleong
• 0
0
votes
1
reply
348
views
News:
Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt
ensembldb
updated 7 days ago by
sophisticated.blackbird.meau
• 0 • written 9 days ago by
Aleena_Ensembl
▴ 30
2
votes
5
replies
867
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 10 days ago by
Thomas
• 0
5
votes
7
replies
2.8k
views
limma correction for tumor purity
limma
10 days ago • updated 4 days ago
gabriella.jacobson-eisenberg
▴ 20
0
votes
1
reply
146
views
FlowSOM is unable to create Output
FlowSOM
updated 10 days ago by
ATpoint
★ 4.8k • written 10 days ago by
marco.klein1
• 0
8
votes
3
replies
2.4k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 8 days ago by
Michael Love
43k • written 10 days ago by
Cassia
▴ 40
2
votes
14
replies
2.7k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
11 days ago • updated 6 days ago
petergrahamclark
• 0
0
votes
4
replies
940
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
12 days ago • updated 6 days ago
sk
• 0
4
votes
6
replies
1.0k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
updated 15 hours ago by
Paul Harrison
▴ 110 • written 13 days ago by
caroline.zanchi
▴ 10
0
votes
1
reply
244
views
Filtering out non-variable probes from EPICv2 matrix
DMRcate
EPICv2manifest
updated 10 days ago by
James W. MacDonald
68k • written 13 days ago by
Sasha
• 0
2
votes
5
replies
1.5k
views
Unable to install a forged BSgenome package
BSgenomeForge
updated 11 days ago by
James W. MacDonald
68k • written 14 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 15 days ago by
James W. MacDonald
68k • written 15 days ago by
Franz Bachmann
• 0
0
votes
3
replies
612
views
Discrepancies in normalised count data vs unnormalised
DESeq2
updated 11 days ago by
swbarnes2
★ 1.4k • written 16 days ago by
AMgroup
• 0
0
votes
2
replies
480
views
Design formula for circadian time-course data for vst() function
DESeq2
17 days ago
Vishnu
• 0
2
votes
5
replies
690
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
19 days ago • updated 1 day ago
massimo
• 0
0
votes
0
replies
241
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
20 days ago
jamiecatalano2
• 0
2
votes
3
replies
1.3k
views
Filtering after DESeq
DESeq2
IHW
updated 11 days ago by
ChaseWendrix
• 0 • written 21 days ago by
caroline.zanchi
▴ 10
0
votes
1
reply
263
views
RNA-seq input to GRaNIE
GRaNIE
updated 22 days ago by
James W. MacDonald
68k • written 22 days ago by
maia.malonzo
• 0
1
vote
3
replies
1000
views
CluserProfiler message "No gene can be mapped"
clusterProfiler
updated 21 days ago by
James W. MacDonald
68k • written 22 days ago by
Carolina
• 0
0
votes
2
replies
600
views
Analyzing TnSeq data with DESeq2
DESeq2
written 23 days ago by
newfunland
• 0
0
votes
2
replies
765
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
23 days ago • updated 1 day ago
Kateřina
• 0
2
votes
1
reply
451
views
ROAST for small sets
limma
mroast
updated 23 days ago by
Gordon Smyth
52k • written 24 days ago by
Jay
• 0
0
votes
2
replies
374
views
RNA Seq using Lrt
DESeq2
24 days ago • updated 23 days ago
Rob
• 0
0
votes
1
reply
112
views
Make DEXSeq plot normal scale
DEXSeq
Dexseq
updated 24 days ago by
James W. MacDonald
68k • written 24 days ago by
Rico
• 0
10
votes
13
replies
1.8k
views
edgeR::cpm() results in negative values from raw counts of 0
edgeR
updated 22 days ago by
Gordon Smyth
52k • written 25 days ago by
Kinnary
▴ 20
0
votes
0
replies
110
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
25 days ago
Shaimaa Gamal
• 0
0
votes
3
replies
982
views
Gene Ontology (GO) Analysis
GOstats
hyperGTest
GO
enrichGO
clusterProfiler
26 days ago • updated 5 days ago
GA
▴ 10
0
votes
0
replies
81
views
GRaNIE with no internet
GRaNIE
29 days ago
maia.malonzo
• 0
2
votes
0
replies
484
views
News:
Bioconductor 3.21 is Released!
devel
release
Release
Devel
29 days ago
shepherl
4.1k
0
votes
2
replies
651
views
Version conflict when pushing to scQTLtools devel branch
Bioconductor
written 4 weeks ago by
XFWu
• 0
0
votes
0
replies
89
views
Issue checking for convergence with the tutorial Dataset. EBseq 2.4.1
EBSeq
4 weeks ago
Javier
• 0
0
votes
3
replies
774
views
Log2foldchange strange behavior
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.8k • written 4 weeks ago by
RambakKulit
• 0
0
votes
0
replies
167
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
5 weeks ago
atlanta
• 0
1
vote
1
reply
1.2k
views
PhD scholar
RNASeqAnalysis
DESeq2
updated 5 weeks ago by
shepherl
4.1k • written 5 weeks ago by
Richa
• 0
0
votes
1
reply
878
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 5 weeks ago by
swbarnes2
★ 1.4k • written 5 weeks ago by
Bioinformatician_R
▴ 20
1
vote
1
reply
1.0k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 5 weeks ago by
ATpoint
★ 4.8k • written 5 weeks ago by
Shaimaa Gamal
• 0
0
votes
1
reply
271
views
Custom CDF creation for HTA 2.0 array using GTF annotation
oligo
oligoClasses
pdInfoBuilder
affycoretools
affyio
5 weeks ago
Seymoo
• 0
46,496 results • Page
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Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Geoff
• 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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