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0
votes
5
replies
2.9k
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DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 5 days ago
Henrik Bengtsson
★ 2.4k
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 7 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
3
replies
793
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 9 months ago by
Hervé Pagès
16k • written 9 months ago by
anavmar1
• 0
0
votes
4
replies
697
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 4 months ago by
Igor
• 0
0
votes
5
replies
3.1k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
0
votes
3
replies
394
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by
Michael Love
42k • written 3 months ago by
ilaria.montali
• 0
1
vote
8
replies
1.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 11 months ago by
sean.mccutcheon
• 0
2
votes
6
replies
1.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 5 weeks ago by
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 10
3
votes
4
replies
234
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 3 days ago by
Gordon Smyth
50k • written 5 days ago by
Chris
• 0
1
vote
3
replies
422
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 19 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 4 months ago by
YNPAN910
• 0 • written 4.7 years ago by
maya.kappil
▴ 30
0
votes
3
replies
466
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
0
votes
2
replies
370
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 9 weeks ago by
ATpoint
★ 4.1k • written 10 weeks ago by
Suvi
• 0
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by
Mingkee
• 0 • written 6.8 years ago by
yura.grabovska
▴ 30
0
votes
4
replies
279
views
DEG with low counts
DESeq2
updated 21 days ago by
Michael Love
42k • written 26 days ago by
Rajat
• 0
1
vote
3
replies
343
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
10 weeks ago • updated 9 weeks ago
I-Hsuan Lin
▴ 10
1
vote
5
replies
580
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 months ago
ilaria.maurizio
• 0
1
vote
4
replies
752
views
MDS plot edgeR
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
jbono
▴ 10
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
65k • written 11 months ago by
kyliecode
• 0
0
votes
2
replies
890
views
News:
List of Deprecated Packages for Bioc3.17
Bioconductor
Deprecation
Devel
devel
13 months ago • updated 11 months 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
2
votes
1
reply
274
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
3 months ago
mat149
▴ 70
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 5 weeks ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage
bsseq
updated 6 months ago by
Adam
• 0 • written 9.7 years ago by
Guest User
★ 13k
0
votes
2
replies
558
views
Accounting for technical replicates in DESeq2
DESeq2
updated 12 months ago by
swbarnes2
★ 1.4k • written 12 months ago by
sara.p
• 0
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago
mohammedtoufiq91
▴ 10
1
vote
7
replies
1.6k
views
enrichGOgradient color change
clusterProfiler
updated 7 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
inna.gur
• 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi
bumphunter
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
src3
• 0
0
votes
4
replies
379
views
Extract LRT results for each comparison
LRT
DESeq2
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Yijing
• 0
1
vote
6
replies
797
views
DelayedArray::read_sparse_block
DelayedArray
updated 7 months ago by
Hervé Pagès
16k • written 8 months ago by
Koki
▴ 10
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by
kledo577
• 0 • written 5.6 years ago by
183227851
• 0
0
votes
5
replies
942
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
7 months ago • updated 6 months ago
dorota.komar
• 0
7
votes
5
replies
7.0k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 7 months ago by
Ke
• 0 • written 2.0 years ago by
kieran.short
▴ 40
0
votes
2
replies
853
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
0
votes
2
replies
827
views
R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 10 months ago by
Michael Love
42k • written 10 months ago by
ikpa_p123
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 10 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
2
replies
424
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 5 months ago by
Stephanie M. Gogarten
▴ 870 • written 5 months ago by
Mindy wang
• 0
2
votes
3
replies
2.2k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 7 weeks ago by
ATpoint
★ 4.1k • written 2.1 years ago by
liqidong52
▴ 20
1
vote
2
replies
3.2k
views
Extract genes from ggvenn?
ggvenn
updated 5 weeks ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
2
replies
489
views
EdgeR FTest
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
nawaz.u.toyama
• 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
3
votes
2
replies
454
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
S
• 0
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges
genomicfeatures
translation
updated 3 months ago by
russ.bainer
▴ 10 • written 8.4 years ago by
madsheilskov
▴ 10
4
votes
6
replies
762
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago
isaac.vock
• 0
1
vote
3
replies
604
views
Read Count Normalisation and validation of analysis
DifferentialExpression
DESeq2
written 4 months ago by
Dinesh
• 0
0
votes
9
replies
850
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
8 months ago
hayleyw
• 0
0
votes
4
replies
3.7k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 10 months ago by
Marco
• 0 • written 4.5 years ago by
mathai.c
• 0
2
votes
2
replies
438
views
Remove duplicates of colData in TreeSummarizedExperiment
dplyr
TreeSummarizedExperiment
updated 7 months ago by
Michael Love
42k • written 7 months ago by
question_guy
• 0
1,741 results • Page
3 of 35
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Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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