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1
vote
0
replies
1.4k
views
EGSEA install licensed KEGG data
EGSEA
KEGG
EGSEAdata
7.9 years ago
john.thompson
▴ 10
2
votes
1
reply
1.6k
views
TopGO - Incorrect mapping genes to GO terms
topgo
go
org.mm.eg.db
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
lehallib
• 0
2
votes
4
replies
1.7k
views
X-axis of MAplot and lfcShrink
deseq2
8.2 years ago • updated 7.9 years ago
Yuya Liang
▴ 20
7
votes
8
replies
3.0k
views
Microarray analysis using RMA method using affy, limma
microarray
annotation
aureus
affy
8.0 years ago • updated 7.9 years ago
neranjan007
• 0
0
votes
1
reply
895
views
Unexpected behavior in Biostrings::pairwiseAlignment
biostrings
updated 7.9 years ago by
Hervé Pagès
16k • written 8.0 years ago by
bc
• 0
5
votes
9
replies
4.3k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
7.9 years ago
emmak
▴ 20
2
votes
3
replies
2.9k
views
Using MAST with DropSeq data
MAST
mast
dropseq
updated 7.9 years ago by
Andrew_McDavid
▴ 280 • written 7.9 years ago by
jeremycfd
▴ 10
0
votes
1
reply
1.8k
views
Analysing microarray raw data: GSEXXXX_non-normalized.txt
lumi
microarray
GSE
updated 7.9 years ago by
Gordon Smyth
53k • written 7.9 years ago by
mkd12
• 0
0
votes
3
replies
1.8k
views
FuntooNorm on 450K and Epic data combined RGSet
funtooNorm
minfi
illuminahumanmethylationepicanno.ilmn10b.hg19
updated 7.9 years ago by
simon_1012
• 0 • written 8.6 years ago by
poojitha.stemcell
▴ 10
1
vote
5
replies
1.6k
views
compare one group to mean of two others in DESeq2 with betaprior=FALSE
deseq2
updated 7.9 years ago by
Michael Love
43k • written 7.9 years ago by
Chris Stubben
▴ 40
1
vote
9
replies
1.4k
views
Compare more than one factor
deseq2
updated 7.9 years ago by
Michael Love
43k • written 7.9 years ago by
Yuya Liang
▴ 20
0
votes
2
replies
1.5k
views
Run tweeDEseq on Flux-capacitor RPKM values
tweedeseq
differential expression
updated 7.9 years ago by
Robert Castelo
★ 3.4k • written 7.9 years ago by
vrehaman
• 0
2
votes
2
replies
4.1k
views
problem using AnnotationDbi
annotationdbi
bioconductor
7.9 years ago
h72ghorashi
• 0
0
votes
0
replies
1.1k
views
methyAnalysis - library(methyAnalysis) hangs when talking to Internet
methyanalysis
7.9 years ago
mcahn
• 0
3
votes
4
replies
2.8k
views
edgeR - comparing treatment groups across multiple populations
rnaseq
edger
updated 7.9 years ago by
Aaron Lun
★ 29k • written 7.9 years ago by
mart1139
• 0
0
votes
4
replies
1.9k
views
Error topGO printGenes
topGo
7.9 years ago
irving.jgalo23
• 0
1
vote
7
replies
2.3k
views
EDGE: Persistent lrt() and odp() command pi0est() error due to low p values
edge
qpcr
qvalue
8.9 years ago • updated 7.9 years ago
joe.d.moore.ii
• 0
0
votes
4
replies
3.0k
views
Problem converting first column to rownames
deseq2
countdata
updated 7.9 years ago by
Michael Love
43k • written 7.9 years ago by
A
▴ 60
2
votes
2
replies
1.3k
views
edgeR - problems with coefficients and decideTests
edger
updated 7.9 years ago by
Aaron Lun
★ 29k • written 7.9 years ago by
trichter
• 0
1
vote
5
replies
2.4k
views
Hm... segfault when using qvalue 1.39.1, has anyone else encountered this?
qvalue
segfault
11.3 years ago • updated 7.9 years ago
Leonardo Collado Torres
★ 1.1k
0
votes
2
replies
1.9k
views
GViz, different group colours
gviz
gviz-package
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
p1990
• 0
3
votes
1
reply
2.0k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 8.0 years ago by
Shamith.Samarajiwa
▴ 180
2
votes
1
reply
5.4k
views
voomWithQualityWeights, design and weights
voom
limma-voom
voomwithqualityweights
rna-seq
updated 7.9 years ago by
Matthew Ritchie
▴ 1000 • written 8.0 years ago by
anne.biton
▴ 20
2
votes
2
replies
1.5k
views
read.delim taking infinite time in edgeR analysis
read.delim
edger
7.9 years ago
fawazfebin
▴ 60
7
votes
2
replies
6.3k
views
getBM error: The query to the BioMart webservice returned an invalid result
biomart
updated 7.9 years ago by
Mike Smith
★ 6.6k • written 7.9 years ago by
Gregulator
▴ 30
1
vote
3
replies
1.1k
views
rna-seq analysis with limma shows only 1 differential expressed gene
limma
rnaseq
updated 7.9 years ago by
chiakivietnam
• 0 • written 8.0 years ago by
jsbng8615
• 0
0
votes
0
replies
955
views
Extracting matched cluster IDs in flowMatch
flowMatch
flow cytometry
7.9 years ago
vinko.tosevski
• 0
0
votes
1
reply
1.4k
views
How to identify Disease biomarkers " DNA sequences as biomarkers "
dnaseq
pathway analysis
protein
biomarkers
7.9 years ago
emadelhewihy
• 0
0
votes
1
reply
1.4k
views
spillover::flowCore problem: Error: Unable to match stains with controls based on intensity: a single stain matches to several multiple controls.
flowCore
spillover
compensation matrix
bioconductor
flow cytometry
7.9 years ago
Samuel Ahuno
• 0
8
votes
2
replies
6.6k
views
qvalue package throws error when used on any p-values but hedenfalk example
qvalue
updated 7.9 years ago by
Storey, John D.
▴ 100 • written 7.9 years ago by
ilikescience1
▴ 40
2
votes
1
reply
2.4k
views
Pathview graph with multiple states/samples or time series
Pathways
graph
Pathways
graph
updated 7.9 years ago by
atanas.kamburov
• 0 • written 12.3 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
1.3k
views
Error using the makeTxDbFromGFF
maketxdbfromgff
7.9 years ago
bright602
• 0
4
votes
7
replies
3.8k
views
DESeq2 vs TCGAbiolinks normalization methods
normalization
rnaseq
deseq2
updated 4.2 years ago by
aristelliger
• 0 • written 8.0 years ago by
array chip
▴ 420
0
votes
5
replies
1.5k
views
Problem converting annotation to GenomicRanges object
genomicranges
7.9 years ago
Anton01
• 0
1
vote
2
replies
1.6k
views
Accessing a local version of BioMart (v0.9) using biomaRt
biomart
R
rest
updated 7.9 years ago by
Mike Smith
★ 6.6k • written 8.0 years ago by
Alex
• 0
1
vote
3
replies
1.9k
views
Comparing Expression Ratios between two genes
limma
updated 7.9 years ago by
Gordon Smyth
53k • written 8.0 years ago by
johnmcma
▴ 10
0
votes
1
reply
1.7k
views
how to set boolean filter
biomart
ensembl
boolean filter
8.0 years ago
shenwei1376
• 0
0
votes
0
replies
1.4k
views
Paired Difference Analysis
metagenomeseq
8.0 years ago
nhua
• 0
0
votes
0
replies
1.4k
views
Job:
Postdoctoral and other positions in bioinformatics, Vanderbilt University, Nashville, USA
machine learning
bioinformatics
data science
circadian rhythms
Job
8.0 years ago
Jake
• 0
0
votes
1
reply
1.3k
views
error when create dba object
diffbind
updated 8.0 years ago by
Rory Stark
★ 5.2k • written 8.0 years ago by
xieyongjun93
• 0
2
votes
6
replies
3.5k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error
cn.mops
updated 22 months ago by
ama304374
• 0 • written 8.0 years ago by
daijieqiong
▴ 10
1
vote
3
replies
1.6k
views
Normalization / size factors of samples with high expression of few genes (viral infection)
deseq2
normalization
sizefactors
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
René
▴ 40
1
vote
6
replies
2.2k
views
Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
BiocGenerics
8.0 years ago
rea
▴ 10
2
votes
2
replies
11k
views
Error: In seq_len(ncol(assay)) : first element used of 'length.out' argument
singlecellexperiment
8.0 years ago
Marina V.V.
• 0
0
votes
1
reply
1.8k
views
DESeq2: same count matrix, different design
deseq2
baseMean
cooks distance
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
da.de
▴ 30
2
votes
13
replies
4.5k
views
Beachmat install / compile issue
beachmat
compilation error
8.0 years ago
daniel.gaffney
▴ 20
0
votes
2
replies
1.2k
views
Error with makeTxDbFromBiomart in GenomicFeatures package
genomicfeatures
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
bright602
• 0
2
votes
1
reply
1.6k
views
DESeq2: multiple genotypes time course
deseq2
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
Matteo Perino
▴ 10
1
vote
2
replies
751
views
Running DESeq2 for different types of data
deseq2
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
yair.gatt
• 0
2
votes
0
replies
1.7k
views
Job:
Full-time bioinformatics instructor position at Fred Hutch
R
shell
Python
SQL
Job
8.0 years ago
ematsen
▴ 20
46,719 results • Page
284 of 935
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Comment: Development of MSstat workflow to analyze DIA time series data
by
Gordon Smyth
53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts)
by
Gordon Smyth
53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package
by
Nguyen
• 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
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A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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