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0
votes
1
reply
1.2k
views
Best Practices for Speeding Up/Optimizing EBIMage
ebimage
7.0 years ago
grockmore
• 0
0
votes
0
replies
822
views
DiffBind - Difficulties construction appropriate consensus set
Diffbind
7.0 years ago
Rob Buurstede
• 0
0
votes
6
replies
2.5k
views
how to achieve reproducibility with BiocParallel regardless of number of threads and OS (set.seed is disallowed)
BiocParallel
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
luluchen
• 0
7
votes
5
replies
2.4k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran
scater
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
heyao
▴ 30
5
votes
1
reply
6.1k
views
RNAseq analysis: what comes first, filtering or normalization
edger
R
rnaseq
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
apfelbapfel
▴ 30
0
votes
0
replies
942
views
A problem about changeCtLayout in HTqPCR
htqpcr
7.0 years ago
tropicalis
• 0
0
votes
0
replies
1.2k
views
ASpli AsDiscover error
R
alternative splicing
ASpli
AsDiscover
7.1 years ago • updated 7.0 years ago
abdul rawoof
▴ 60
1
vote
8
replies
2.2k
views
DESeq2 model design for paired samples with multiple factors
deseq2
rnaseq
model design
7.1 years ago • updated 7.0 years ago
swillis4
▴ 10
0
votes
0
replies
687
views
regionR randomizeRegions allow.overlaps option
regionR
7.0 years ago
crysis405
▴ 10
0
votes
1
reply
1.5k
views
Gene similarity by GOSemSim
gosemsim
mgenesim
7.0 years ago
athirak1986
• 0
0
votes
0
replies
1.7k
views
vcf to venn diagram
snps
vcf
venn diagram
ggplot2
7.0 years ago
mictadlo
▴ 10
3
votes
4
replies
2.6k
views
Implications of TMM Normalization and Possible Alternatives
edger
TMM
DEG
normalization
updated 7.0 years ago by
Gordon Smyth
53k • written 7.1 years ago by
rproendo
▴ 30
1
vote
2
replies
2.9k
views
Gviz: Setting Up Colour / Fill for AnnotationTrack (strand-dependent colour)
Gviz
gviz-package
GFF
annotationtrack
strand-dependent
updated 7.0 years ago by
Robert Ivanek
▴ 750 • written 7.0 years ago by
JezDD
• 0
0
votes
0
replies
928
views
Error in base::strsplit(x, ...) : non-character argument
software error
r
readComp {systemPipeR}
7.0 years ago
catscampos
• 0
3
votes
3
replies
3.7k
views
Gene ID to Gene Name/Symbol in loom files
Scater
LoomR
SCopeloomR
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
Abhishek Singh
▴ 20
0
votes
0
replies
1.5k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker
chipseq
7.1 years ago
bioinfouser2
▴ 10
1
vote
1
reply
1.5k
views
tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DESeq2
tximport
deseq2
rnaseq
3' tagged RNA
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
rbenel
▴ 50
2
votes
3
replies
1.1k
views
CalcNormFactors in Edge r
edger
updated 7.1 years ago by
Gordon Smyth
53k • written 7.1 years ago by
phickner2
• 0
0
votes
0
replies
1.2k
views
ggbio error when following tutorial, ideogram not highlighted, genetrack not working
ggbio
ideogram
autoplot
7.1 years ago
gpwhiz
▴ 10
0
votes
1
reply
1.6k
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
Jakub
▴ 50
1
vote
4
replies
2.0k
views
Error in `rownames : Gviz plotTracks
gviz
plottracks
generegiontrack
7.1 years ago
gpwhiz
▴ 10
2
votes
2
replies
1.6k
views
Different results from limma depending on whether or not I have an intercept term in my model
limma
lmfit
voom
limma design matrix
voomwithqualityweights
updated 7.1 years ago by
Gordon Smyth
53k • written 7.1 years ago by
kediggins
▴ 10
0
votes
0
replies
668
views
CRLMM R package question: 0%Error in CRLMM: Error in quantile.default(M, c(1, 5)/6, names = FALSE)
bioconductor
7.1 years ago
junyi
• 0
3
votes
7
replies
5.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
Yonatan Amzaleg
• 0
1
vote
3
replies
1.5k
views
Installing SigneR problem
signer
install error
updated 7.1 years ago by
shepherl
4.3k • written 7.1 years ago by
taha.valizadeh
• 0
1
vote
3
replies
2.1k
views
Explanation of Coefficients in DESeq2
deseq2
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
coyoung
▴ 10
0
votes
9
replies
1.6k
views
Genes that have NOT changed
deseq2
7.1 years ago
evocanres
• 0
1
vote
1
reply
1.4k
views
error: incorrect number of fields (1) input.bam:1
shortread
readaligned
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
kspata
▴ 10
2
votes
5
replies
5.4k
views
GDCdownload does not work
GDCdow
tcgabiolinks
error
tcgadownload
download_error
updated 7.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.1 years ago by
miki716
• 0
0
votes
3
replies
1.1k
views
biotmle package error with heatmap/dendrogram
biotmle
updated 7.1 years ago by
nhejazi
• 0 • written 7.1 years ago by
detroit.drive
• 0
1
vote
6
replies
3.7k
views
DESeq2 unbalanced sample size
deseq2
bioconductor
bioinformatics
statistics
updated 2.9 years ago by
Michael Love
43k • written 7.1 years ago by
casikecola
• 0
0
votes
1
reply
1.1k
views
DESeq2 modeling different organisms as batch effects
deseq2
batch effect
across species
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
mjldehoon
• 0
1
vote
1
reply
4.9k
views
compareCluster on Mus musculus
clusterprofiler
7.1 years ago
unamourdeswann
▴ 10
0
votes
1
reply
1.8k
views
SC3 how to customize plots ?
SC3
plot
consensus
marker
heatmap
updated 7.1 years ago by
Vladimir Kiselev
▴ 150 • written 7.1 years ago by
shaktirielland
• 0
0
votes
1
reply
3.5k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater
seurat
singlecellexperiment
rnaseq
updated 7.1 years ago by
Gordon Smyth
53k • written 7.1 years ago by
hamza_karakurt
▴ 60
4
votes
2
replies
1.6k
views
Speed efficient way to select the n-th element from GRangsList
R
GenomicRanges
IRanges
7.1 years ago
foehn
▴ 100
4
votes
11
replies
2.3k
views
News:
Bioconductor 3.8 is released
bioconductor
news
release
News
updated 7.1 years ago by
restat110
• 0 • written 7.2 years ago by
Valerie Obenchain
★ 6.8k
1
vote
2
replies
1.9k
views
prepDE KeyError on MSTRG
deseq2
prepDE
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
shintzen
• 0
0
votes
2
replies
1.1k
views
Remove "no_feature" and "alignment_not_unique" counts before using EdgeR or Deseq2
edger
deseq2
updated 7.1 years ago by
Gordon Smyth
53k • written 7.1 years ago by
cottrellka
• 0
0
votes
5
replies
1.8k
views
DEXSeq 1.26.0 running very slowly (stuck?)
dexseq
7.1 years ago
Lance Parsons
• 0
2
votes
4
replies
3.3k
views
error: namespace Loading DESeq2
deseq2
error namespace
biobase
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
jpcourneya
• 0
1
vote
5
replies
3.0k
views
error while using champ.svd() function
champ
7.1 years ago
sinha.puja
▴ 10
1
vote
1
reply
1.9k
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna
weighted correlation network analysis
correlation matrix
scale-free topology
metagenomics
updated 7.1 years ago by
Peter Langfelder
★ 3.0k • written 7.1 years ago by
eneas_aguirre
• 0
1
vote
7
replies
2.0k
views
paired sample - SVA model matrix
limma
sva
paired sample
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
flippy23
• 0
0
votes
1
reply
2.6k
views
Error with DEseq2: DESeqDataSetFromMatrix. error indicating row names of the colData are not in the same order as the colnames of the countData
deseq2
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
lara
• 0
0
votes
0
replies
1.3k
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
7.1 years ago
mstagliamonte
▴ 10
0
votes
2
replies
1.5k
views
DropletUtils barcodeRanks bug (?)
dropletutils
updated 7.1 years ago by
Aaron Lun
★ 29k • written 7.1 years ago by
jmanning
• 0
2
votes
5
replies
4.8k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
dorothy.jrobbert
▴ 30
0
votes
3
replies
959
views
printtiploess error from normalizeWthinArrays
limma
updated 7.1 years ago by
Gordon Smyth
53k • written 21.8 years ago by
Susan Renn
▴ 20
1
vote
9
replies
35k
views
salmon output for DESeq2 analysis
DESeq2
7.1 years ago
capricygcapricyg
▴ 10
46,712 results • Page
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Comment: Incosistencies in buildSNNGraph() function
by
ATpoint
★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function
by
Aaron Lun
★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
TikTsokaas33ocissalpc
• 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
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Answer: Incosistencies in buildSNNGraph() function
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