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9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.2 years ago by
tangming2005
▴ 190
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 22 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 11 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
2
votes
28
replies
4.3k
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 16 months ago by
Manmohit
▴ 10
5
votes
25
replies
827
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 21 days ago by
Gordon Smyth
50k • written 4 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
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 14 months ago by
Poonam
• 0
8
votes
23
replies
858
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 15 days ago by
Robert Castelo
★ 3.3k • written 16 days ago by
Bine
▴ 40
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
28 days ago • updated 6 days ago
Chris
• 0
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 9 weeks ago by
Michael Love
41k • written 7.8 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
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
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 2.2 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 3 months ago by
Matthias Lienhard
▴ 240 • written 7.1 years ago by
justinburgener
▴ 20
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 9 days ago
shepherl
3.8k
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
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
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 8.9 years ago by
Pauly Lin
▴ 150
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
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
3.8k • written 2.8 years ago by
S
▴ 10
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 6 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
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 2.0 years ago by
Dina
▴ 50
2
votes
15
replies
663
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 10 weeks ago by
Michael Love
41k • written 11 weeks ago by
cinzia.spagnoli
• 0
8
votes
15
replies
1.4k
views
PCA percent variance DESeq2
PCA
DESeq2
8 months ago
IUH
• 0
1
vote
15
replies
8.1k
views
Exporting DESeq2 filtered results
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 3.2 years ago by
Laura
▴ 10
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
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
0
votes
14
replies
1.8k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 12 weeks ago by
nguyen
• 0 • written 8 months ago by
Deepa
• 0
4
votes
14
replies
3.4k
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
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
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
3
votes
13
replies
1.3k
views
Timely differentially expressed genes
timecoursedata
limma
7 months ago • updated 5 months ago
triZZla
• 0
0
votes
13
replies
667
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 8 weeks ago by
Michael Love
41k • written 9 weeks ago by
r.r.bioinf
• 0
9
votes
13
replies
6.4k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 4.0k • written 2.1 years ago by
nhaus
▴ 30
1
vote
13
replies
879
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
4
votes
13
replies
1.8k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 6 months ago by
Hervé Pagès
16k • written 2.6 years ago by
Koki
▴ 10
8
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
Chris
• 0
1
vote
13
replies
278
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
5 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
8
votes
12
replies
2.5k
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
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
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 4 days ago
shepherl
3.8k
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
12
votes
12
replies
788
views
Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by
Robert Castelo
★ 3.3k • written 6 days ago by
Chris
• 0
1
vote
12
replies
1.0k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
9 weeks ago • updated 8 weeks ago
paria.alipour
• 0
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 7 months ago by
Miguel
• 0 • written 3.2 years ago by
robert.chen
• 0
4
votes
12
replies
932
views
Ensembl down???
biomaRt
5 months ago • updated 4 months ago
bas_work
▴ 30
1,740 results • Page
1 of 35
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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