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9
votes
38
replies
6.5k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.1 years ago by
tangming2005
▴ 190
7
votes
32
replies
5.1k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 5 weeks ago by
Emmi
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
2
votes
28
replies
4.2k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 4 months ago by
James W. MacDonald
65k • written 15 months ago by
Manmohit
▴ 10
7
votes
28
replies
6.0k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 7 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.0 years ago by
fiona.dick91
▴ 60
0
votes
25
replies
2.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 3 months ago by
Michael Love
41k • written 13 months ago by
Poonam
• 0
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 5 weeks ago by
Michael Love
41k • written 7.8 years ago by
adesrichard
▴ 30
0
votes
21
replies
6.5k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 4 months ago by
Marge
• 0 • written 11.2 years ago by
José Luis Lavín
▴ 280
0
votes
21
replies
2.3k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
28
votes
21
replies
47k
views
deseq2 filter the low counts
deseq2
lowcount
updated 10 weeks ago by
Xiao
• 0 • written 9.1 years ago by
aristotele_m
▴ 40
1
vote
20
replies
1.9k
views
Time-course, comparison of two groups
edgeR
12 months ago • updated 11 months ago
boczniak767
▴ 720
5
votes
19
replies
5.7k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 7 months ago by
liz.lamarca
• 0 • written 2.7 years ago by
kwangbom
▴ 10
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 12 weeks ago by
Matthias Lienhard
▴ 240 • written 7.0 years ago by
justinburgener
▴ 20
5
votes
18
replies
7.3k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 3 months ago by
picasa1983
• 0 • written 2.2 years ago by
Victor
• 0
0
votes
17
replies
3.3k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 9 months ago by
snow34
• 0 • written 6.5 years ago by
ap3637
• 0
2
votes
17
replies
842
views
Problem installing package, version of dependency issue
AnnotationDbi
GO.db
updated 9 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 10 weeks ago by
alexandre.blais
▴ 50
2
votes
17
replies
1.6k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 10 months ago by
Michael Love
41k • written 10 months ago by
Alina
• 0
9
votes
16
replies
1.6k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
11 months ago
Chris
• 0
3
votes
16
replies
2.0k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 9 weeks ago by
shepherl
3.8k • written 2.7 years ago by
S
▴ 10
3
votes
16
replies
17k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 9 months ago by
Robert
• 0 • written 8.9 years ago by
samuel collombet
▴ 140
1
vote
16
replies
3.1k
views
error in ChAMP loading file
ChAMP
updated 16 days ago by
hortenseguillaume96
• 0 • written 16 months ago by
Giulia
• 0
4
votes
16
replies
7.2k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 7 days ago by
Shaimaa Gamal
• 0 • written 8.9 years ago by
Pauly Lin
▴ 150
5
votes
15
replies
1.4k
views
how can I do gene differential analysis on data after vst
DESeq2
written 12 months ago by
linouhao
▴ 20
2
votes
15
replies
523
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 6 weeks ago by
Michael Love
41k • written 7 weeks ago by
cinzia.spagnoli
• 0
8
votes
15
replies
1.3k
views
PCA percent variance DESeq2
PCA
DESeq2
7 months ago
IUH
• 0
5
votes
15
replies
4.9k
views
Cross-species RNA-seq with DESeq2
deseq2
rnaseq
across species
updated 9 months ago by
James W. MacDonald
65k • written 6.7 years ago by
vtartaglio
▴ 10
1
vote
15
replies
7.8k
views
Exporting DESeq2 filtered results
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 3.1 years ago by
Laura
▴ 10
3
votes
15
replies
2.6k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 10 days ago
shepherl
3.8k
22
votes
15
replies
7.2k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 4 months ago by
Marie
▴ 10 • written 23 months ago by
Dina
▴ 50
0
votes
14
replies
1.6k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 8 weeks ago by
nguyen
• 0 • written 7 months ago by
Deepa
• 0
4
votes
14
replies
3.3k
views
Data input for aracne2regulon function in viper package
viper
updated 11 weeks ago by
YNPAN910
• 0 • written 4.6 years ago by
maya.kappil
▴ 30
2
votes
14
replies
1.0k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Jerina
▴ 10
7
votes
13
replies
1.7k
views
Interpret plot from DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Chris
• 0
1
vote
13
replies
783
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions
replicates
SmallRNAData
DESeq2
updated 11 weeks ago by
Kevin Blighe
★ 3.9k • written 3 months ago by
samer
▴ 10
0
votes
13
replies
585
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 29 days ago by
Michael Love
41k • written 5 weeks ago by
r.r.bioinf
• 0
8
votes
13
replies
2.6k
views
Help with Error in DiffBind
DiffBind
ATACSeq
12 months ago
Chris
• 0
3
votes
13
replies
1.2k
views
Timely differentially expressed genes
timecoursedata
limma
6 months ago • updated 4 months ago
triZZla
• 0
4
votes
13
replies
1.7k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 5 months ago by
Hervé Pagès
16k • written 2.5 years ago by
Koki
▴ 10
1
vote
13
replies
10k
views
unable to access index for repository
Bioconductor
ConsensusClusterPlus
updated 7 months ago by
Mehdi
• 0 • written 15 months ago by
k.wickstrom
• 0
9
votes
13
replies
6.0k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 7 weeks ago by
ATpoint
★ 4.0k • written 2.0 years ago by
nhaus
▴ 10
4
votes
13
replies
1.2k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 months ago by
Michael Love
41k • written 7 months ago by
Christian
• 0
4
votes
12
replies
3.6k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 6 months ago by
Miguel
• 0 • written 3.1 years ago by
robert.chen
• 0
8
votes
12
replies
2.4k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 10 months ago by
Michael Love
41k • written 11 months ago by
Michael Steinbaugh
▴ 90
1
vote
12
replies
2.2k
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 9 weeks ago by
Mary
• 0 • written 2.4 years ago by
Ming
▴ 380
4
votes
12
replies
817
views
Ensembl down???
biomaRt
4 months ago • updated 3 months ago
bas_work
▴ 30
1
vote
12
replies
2.6k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 5 months ago by
Assa Yeroslaviz
★ 1.5k • written 20 months ago by
Maryam.sed1400
• 0
3
votes
12
replies
2.0k
views
t.test to determine the P-value in DESeq2
DESeq2
written 17 months ago by
Maryam.sed1400
• 0
1
vote
12
replies
962
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
5 weeks ago • updated 4 weeks ago
paria.alipour
• 0
3
votes
12
replies
1.3k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 11 months ago by
Michael Love
41k • written 11 months ago by
urwah
▴ 10
2
votes
12
replies
1.1k
views
P-value inflation?
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
dsambo
▴ 10
1,736 results • Page
1 of 35
Recent ...
Replies
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
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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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