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4
votes
2
replies
1.4k
views
Splatter: simulating fold changes for specific genes?
splatter
7.2 years ago
Brian Haas
▴ 90
1
vote
3
replies
1.9k
views
News:
Initial List of Deprecated Package Bioc 3.9
package
deprecate
release
News
updated 7.2 years ago by
Wolfgang Huber
★ 13k • written 7.2 years ago by
shepherl
4.3k
0
votes
9
replies
2.6k
views
unable to load rsbml for piano reporter metabolite analysis
rsbml
piano
libsbml
gene set enrichment analysis
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
jan.strauss
• 0
1
vote
1
reply
905
views
batch effect - Limma package
limma
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
dressa_ol
• 0
1
vote
6
replies
3.1k
views
DESeq2: two genotypes, one treatment
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
David ROUX
▴ 20
2
votes
1
reply
1.2k
views
DNAStringSet to DNAStringSetList according to pattern in sequence names
dnastringset
dnastringsetlist
seqnames
7.2 years ago
s.ghignone
▴ 10
0
votes
1
reply
1.5k
views
RNAseq gene expression analysis in Personalized genomics
TCGA
deseq2
edger
limma
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
bioc.vkas
• 0
6
votes
5
replies
2.0k
views
dmrseq installation failed
installation problem
dmrseq
bumphunter
updated 7.2 years ago by
shepherl
4.3k • written 7.2 years ago by
guy.bioinfo
▴ 10
0
votes
1
reply
1.5k
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
FaisalH
• 0
0
votes
2
replies
2.7k
views
determine k during RUVSeq
ruvseq
updated 7.2 years ago by
davide risso
▴ 980 • written 7.2 years ago by
capricygcapricyg
▴ 10
0
votes
6
replies
2.2k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq
alternative splicing
SGSeq
7.2 years ago
andrea.bast
• 0
0
votes
0
replies
888
views
alphabet/encoding IlluminaQuality SolexaQuality
Biostrings
XStringQuality
7.2 years ago
felix.ernst
• 0
0
votes
2
replies
1.4k
views
Pull out sequences between ranges?
getsequence
updated 7.2 years ago by
roxys9150
• 0 • written 7.2 years ago by
Teeps
• 0
2
votes
1
reply
1.5k
views
Best practices for CRAN package calling a Bioconductor package function
cran
package development
dependencies
updated 7.2 years ago by
Peter Langfelder
★ 3.0k • written 7.2 years ago by
bjgrant
• 0
0
votes
5
replies
2.7k
views
salmon output file for differential expression analysis
salmon rna seq
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Bob
• 0
0
votes
0
replies
1.3k
views
xlim not working with ggbio
ggbio
7.2 years ago
marisa.e.miller
• 0
1
vote
1
reply
1.5k
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis
pcrrelate
gds
updated 7.2 years ago by
Stephanie M. Gogarten
▴ 890 • written 7.2 years ago by
roll
• 0
3
votes
16
replies
3.3k
views
Internal bug of DMR-Seq?
dmrseq
updated 7.2 years ago by
keegan
▴ 60 • written 7.3 years ago by
kuckunniwid
• 0
1
vote
0
replies
953
views
Job:
Computational biologist/bioinformatician for translational cancer research
job
Job
7.2 years ago
falcomata.c
▴ 10
2
votes
2
replies
1.8k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger
design matrix
glmlrt()
glmQFTest()
paired design
7.2 years ago
oakhamwolf
• 0
0
votes
2
replies
766
views
"mogene10stv1cdf"
updated 7.2 years ago by
daveoscar3232
• 0 • written 15.8 years ago by
Luqin Deng
▴ 10
0
votes
1
reply
1.4k
views
Creating a design matrix
design matrix
limma
updated 7.2 years ago by
Gordon Smyth
53k • written 7.4 years ago by
mahm
▴ 20
1
vote
3
replies
2.2k
views
Remove reads from raw fastq
shortread
biostrings
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
ferbecneu
• 0
3
votes
3
replies
1.7k
views
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger
differential gene expression
glmtreat
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
svlachavas
▴ 840
2
votes
1
reply
1.4k
views
tximeta remote versus local reference files
tximeta
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
igor
▴ 50
2
votes
2
replies
1.6k
views
p -values smaller than machine epsilon in edgeR
edger
p values
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
oscarf
• 0
0
votes
3
replies
1.3k
views
p-values smaller than machine epsilon in DESeq2
deseq2
pvalue
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
oscarf
• 0
1
vote
1
reply
1.5k
views
GenomicFeatures won't install for 3.8 release
installation
biocmanager
updated 7.2 years ago by
shepherl
4.3k • written 7.2 years ago by
Michael Steinbaugh
▴ 90
3
votes
2
replies
1.6k
views
EdgeR - blocking for multiple factors at once - Errors
EdgeR
multiple factor design
blocked design
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
D
▴ 10
0
votes
2
replies
1.3k
views
Question re "Group-specific condition effects, individuals nested within groups"
deseq2
linear model
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
fnigsch
• 0
11
votes
5
replies
3.5k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom
duplicatecorrelation
random effects
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
tcalvo
▴ 100
2
votes
3
replies
1.3k
views
Human Exon: arome.affymetrix residuals Inf value
exons
exon array analysis
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
GENOMIC_region
• 0
1
vote
2
replies
1.7k
views
Split AME .tsv file into GRanges object or DataFrame
meme
ame
motif
dataframe
granges
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
rbronste
▴ 60
0
votes
0
replies
837
views
FourCseq extraction of fragments
fourcseq
7.2 years ago
ferbecneu
• 0
0
votes
1
reply
1.8k
views
Use DiffBind to find differential peaks among multiple cell types
diffbind
atac-seq
differential analysis
deseq2
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
duvaller
• 0
1
vote
1
reply
1.2k
views
How to color different column bars independently using dba.plotHeatmap (DiffBind)?
diffbind
dba.plotHeatmap
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
Gary
▴ 20
0
votes
1
reply
1.0k
views
adding a new consensus peakset question
diffbind
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
yuhongning2013
• 0
1
vote
7
replies
4.0k
views
limma and intercept
limma
intercept
7.2 years ago
Nicolas Servant
▴ 260
3
votes
2
replies
2.0k
views
diffbind finding not differential site
diffbind
chipseq
histone chip-seq
differential binding analysis
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
woongjaej
• 0
3
votes
2
replies
2.9k
views
biomaRt question (missing gene information?)
biomart
R
updated 7.2 years ago by
Mike Smith
★ 6.6k • written 7.2 years ago by
Mike
▴ 10
4
votes
5
replies
1.9k
views
Can't push upstream - duplicate commits
git
updated 7.2 years ago by
Mike Smith
★ 6.6k • written 7.2 years ago by
spollack
• 0
0
votes
4
replies
1.2k
views
DESeq2 Multi-Sample Test
deseq2
updated 7.2 years ago by
swbarnes2
★ 1.4k • written 7.2 years ago by
jonathan.diedrich
• 0
0
votes
4
replies
2.4k
views
csaw spike-in normalization
ChIP-seq
csaw
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
Nicolas Servant
▴ 260
0
votes
4
replies
1.5k
views
DESeq2 MA plot normalisation Issue
deseq2
normalization
maplot
rnaseq
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
ma619
• 0
0
votes
3
replies
956
views
Could GenomicFeature include genes that are on multiple chromosomes?
GenomicFeature
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
hxlei613
• 0
1
vote
11
replies
4.2k
views
edgeR package fails to load after install
edger
install error
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
jenny.russ
• 0
8
votes
13
replies
3.0k
views
RSVSim insertions from chr1 to chr2
rsvsim
7.2 years ago
FDG
▴ 70
1
vote
0
replies
1.5k
views
Job:
2 Postdoc and 2 PhD positions in Regulatory genomics / Rare disease Gagneur lab, TU Munich
genomics
genetics
machine learning
Job
7.2 years ago
gagneur
▴ 10
1
vote
2
replies
902
views
Any way to get a p-value for multiple comparisons in DESeq2?
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Raymond
▴ 20
0
votes
5
replies
3.7k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R
annotation
ensembldb
7.2 years ago
foehn
▴ 100
46,712 results • Page
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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…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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Comment: Guitar R package requires update due to dependency GenomicFeatures
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