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9
votes
38
replies
6.8k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.2 years ago by
tangming2005
▴ 190
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 28 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 12 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
2
votes
28
replies
4.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 5 months ago by
James W. MacDonald
65k • written 17 months ago by
Manmohit
▴ 10
0
votes
25
replies
2.3k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 4 months ago by
Michael Love
41k • written 15 months ago by
Poonam
• 0
5
votes
25
replies
871
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
8
votes
23
replies
913
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 21 days ago by
Robert Castelo
★ 3.3k • written 22 days ago by
Bine
▴ 40
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 10 weeks ago by
Michael Love
41k • written 7.9 years ago by
adesrichard
▴ 30
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 5 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Xiao
• 0 • written 9.2 years ago by
aristotele_m
▴ 40
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 15 days ago
shepherl
3.9k
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 4 months ago by
picasa1983
• 0 • written 2.3 years ago by
Victor
• 0
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 4 months ago by
Matthias Lienhard
▴ 240 • written 7.1 years ago by
justinburgener
▴ 20
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
2
votes
17
replies
1.0k
views
Problem installing package, version of dependency issue
AnnotationDbi
GO.db
updated 3 months ago by
Lluís Revilla Sancho
▴ 730 • written 3 months ago by
alexandre.blais
▴ 50
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Alina
• 0
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 10 months ago by
Robert
• 0 • written 9.0 years ago by
samuel collombet
▴ 140
3
votes
16
replies
2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by
shepherl
3.9k • written 2.8 years ago by
S
▴ 10
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 5 weeks ago by
Shaimaa Gamal
• 0 • written 9.0 years ago by
Pauly Lin
▴ 150
22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 5 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
2
votes
15
replies
688
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 11 weeks ago by
Michael Love
41k • written 12 weeks ago by
cinzia.spagnoli
• 0
8
votes
15
replies
1.5k
views
PCA percent variance DESeq2
PCA
DESeq2
8 months ago
IUH
• 0
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2
rnaseq
across species
updated 10 months ago by
James W. MacDonald
65k • written 6.8 years ago by
vtartaglio
▴ 10
1
vote
15
replies
8.1k
views
Exporting DESeq2 filtered results
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 3.2 years ago by
Laura
▴ 10
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 3 months ago by
YNPAN910
• 0 • written 4.7 years ago by
maya.kappil
▴ 30
0
votes
14
replies
1.9k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by
nguyen
• 0 • written 8 months ago by
Deepa
• 0
2
votes
14
replies
1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Jerina
▴ 10
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor
ConsensusClusterPlus
updated 8 months ago by
Mehdi
• 0 • written 16 months ago by
k.wickstrom
• 0
3
votes
13
replies
1.4k
views
Timely differentially expressed genes
timecoursedata
limma
7 months ago • updated 5 months ago
triZZla
• 0
0
votes
13
replies
680
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 9 weeks ago by
Michael Love
41k • written 10 weeks ago by
r.r.bioinf
• 0
1
vote
13
replies
902
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions
replicates
SmallRNAData
DESeq2
updated 3 months ago by
Kevin Blighe
★ 3.9k • written 4 months ago by
samer
▴ 10
9
votes
13
replies
6.5k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 12 weeks ago by
ATpoint
★ 4.1k • written 2.1 years ago by
nhaus
▴ 30
8
votes
13
replies
1.9k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
Chris
• 0
4
votes
13
replies
1.8k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 7 months ago by
Hervé Pagès
16k • written 2.6 years ago by
Koki
▴ 10
1
vote
13
replies
369
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 7 days ago
fernanda.backsouza
▴ 10
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 months ago by
Michael Love
41k • written 8 months ago by
Christian
• 0
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 10 days ago
shepherl
3.9k
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by
Michael Love
41k • written 12 months ago by
Michael Steinbaugh
▴ 90
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 14 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
2
votes
12
replies
1.3k
views
P-value inflation?
DESeq2
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
dsambo
▴ 10
1
vote
12
replies
2.4k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 3 months ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
4
votes
12
replies
958
views
Ensembl down???
biomaRt
5 months ago • updated 4 months ago
bas_work
▴ 30
3
votes
12
replies
2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by
Maryam.sed1400
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0
by
James W. MacDonald
65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
fatinataly
• 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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