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Job:
Bioinformatics Postdoc in Functional Evolutionary Genomics, Heidelberg, Germany
rnaseq
genomics
evolution
Job
9.8 years ago
henrik.kaessmann
• 0
0
votes
2
replies
1.7k
views
on extend_val parameter in parseWorkspace
flowworkspace
updated 9.8 years ago by
Jiang, Mike
★ 1.3k • written 9.8 years ago by
lovetatting
▴ 10
0
votes
1
reply
1.4k
views
Problem installing RBGL
rbgl
boost
9.8 years ago
tzintzuni
• 0
1
vote
3
replies
1.3k
views
Extract information from GenomicRanges
genomicranges
genomicfeatures
9.8 years ago
ribioinfo
▴ 100
3
votes
4
replies
3.5k
views
DESeq is better than DESeq2?
deseq2
deseq
9.8 years ago
ribioinfo
▴ 100
9
votes
6
replies
3.8k
views
Any method can coerce "list" object to GRanges [reproducible example is included]?
granges
error handling
R
updated 9.8 years ago by
Michael Lawrence
★ 11k • written 9.8 years ago by
Jurat Shahidin
▴ 80
0
votes
0
replies
1.3k
views
Regarding the package RankProd
microarray
rankprod
9.8 years ago
sancharisircar24
• 0
3
votes
7
replies
5.3k
views
edgeR glmLRT and interaction effect: an example
rna-seq
edger
glmlrt
interactions
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
David R
▴ 90
2
votes
1
reply
2.4k
views
Trouble parsing a workspace in flowWorkspace
flowworkspace
opencyto
updated 9.8 years ago by
lovetatting
▴ 10 • written 9.8 years ago by
wir.traumen
▴ 10
0
votes
2
replies
1.8k
views
Cannot replicate circle plot vignette output in ggbio devel
software error
ggbio
circle plot
updated 9.8 years ago by
Michael Lawrence
★ 11k • written 9.8 years ago by
davis
▴ 90
1
vote
5
replies
1.6k
views
Question about contrast matrix using limma
limma
rna-seq
limma contrast matrix
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
lestelles
• 0
3
votes
2
replies
2.6k
views
DESEQ2 (R) design/contrast formula questions
deseq2
phyloseq
multiple factor design
paired samples
updated 9.8 years ago by
mcmurdie
▴ 20 • written 9.8 years ago by
pete_bioinfo
▴ 10
0
votes
1
reply
1.8k
views
maSigPro edesign and error message
masigpro
9.8 years ago
simonjean434
▴ 10
1
vote
3
replies
3.8k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.8 years ago
philipp24
▴ 30
3
votes
7
replies
2.4k
views
To find Differential expressed exons using xps package
xps
exons
updated 9.8 years ago by
cstrato
★ 3.9k • written 9.8 years ago by
Biologist
▴ 120
2
votes
1
reply
2.0k
views
VariantAnnotation as.vranges with asterisk in ALT field
variantannotation
gatk
updated 9.8 years ago by
Michael Lawrence
★ 11k • written 9.8 years ago by
Jeremy Leipzig
▴ 70
2
votes
1
reply
3.2k
views
Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?
gviz
9.8 years ago
stianlagstad
▴ 90
5
votes
12
replies
3.0k
views
Filtering before the linear modelling and empirical bayes steps
DEG
Limma
Filtering
updated 9.8 years ago by
Ryan C. Thompson
★ 7.9k • written 9.9 years ago by
Shamim Sarhadi
▴ 20
5
votes
5
replies
3.3k
views
Accounting for 5'/3' Bias in DESeq 2
deseq2
updated 9.8 years ago by
Ryan C. Thompson
★ 7.9k • written 9.8 years ago by
Jakub
▴ 50
2
votes
1
reply
1.0k
views
how to design contrast formula in different developemntal stage
EdgeR
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
simonjean434
▴ 10
0
votes
3
replies
5.1k
views
DESeq2, Still a most genes get padj=NA after declare cooksCutoff=FALSE in the results () function
deseq2
NA
cooksCutoff
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
colaneri
▴ 30
2
votes
2
replies
1.5k
views
Subset DEXSeqDataSet In DEXSeq
dexseq
9.8 years ago
adelmane
▴ 20
6
votes
25
replies
5.0k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps
heatmap
limma
updated 9.8 years ago by
cstrato
★ 3.9k • written 9.8 years ago by
Biologist
▴ 120
0
votes
3
replies
3.4k
views
Questions about analysis of Human Gene 2.0 ST Array
oligo
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
Biologist
▴ 120
1
vote
3
replies
2.1k
views
Givz sashimi plot controlling the height of plots.
gviz
sashimi plots
updated 9.8 years ago by
Robert Ivanek
▴ 750 • written 9.8 years ago by
r.a.lowe1
• 0
1
vote
2
replies
1.7k
views
Multiple transcription factors over expression analysis
deseq2
rnaseq
9.8 years ago
sebastiano.curreli
• 0
4
votes
4
replies
4.1k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 9.8 years ago by
James W. MacDonald
68k • written 9.9 years ago by
AST
▴ 60
0
votes
1
reply
1.1k
views
modeling tissue effect
deseq2
9.8 years ago
tony.fox2016
▴ 40
3
votes
3
replies
4.5k
views
missMethyl: Gene ontology analysis
missMethyl
9.9 years ago • updated 9.8 years ago
philipp24
▴ 30
0
votes
0
replies
1.6k
views
Pathway analysis of differentially methylated CpGs
limma
missmethyl
9.8 years ago
philipp24
▴ 30
0
votes
6
replies
4.0k
views
TCGAbiolinks DNA methylation analysis TCGAvisualize_meanMethylation
tcgabiolinks
updated 9.8 years ago by
Tiago C. Silva
▴ 270 • written 9.8 years ago by
maedakus
▴ 10
0
votes
2
replies
1.4k
views
Error when trying to load a gff3 with GenomicFeatures
genomicfeatures
updated 9.8 years ago by
Mike Smith
★ 6.6k • written 9.8 years ago by
gil.hornung
• 0
1
vote
2
replies
1.7k
views
[gwascat] makeCurrentGwascat() fails
gwascat
9.8 years ago
enricoferrero
▴ 680
0
votes
0
replies
1.2k
views
Can we expand the dimensions of dataset infinitely in RHDF5?
RHDF5
9.8 years ago
kunalpurimkbk
• 0
0
votes
2
replies
2.7k
views
Help with toGRanges
granges
chippeakanno
updated 9.8 years ago by
Dario Strbenac
★ 1.6k • written 9.8 years ago by
mhartman3
• 0
0
votes
2
replies
1.1k
views
Agilent cgh data read and normalized
normalization
updated 9.8 years ago by
Dario Strbenac
★ 1.6k • written 9.8 years ago by
sainiisha22
• 0
1
vote
2
replies
2.1k
views
Combining GRange/VRange objects
granges
vranges
readvcfasvranges
somaticsignatures
updated 9.8 years ago by
Michael Lawrence
★ 11k • written 9.8 years ago by
jpluta26
• 0
1
vote
1
reply
1.5k
views
Adding legends to sushi plots produced using plotBed function
sushi
plotBed
updated 9.8 years ago by
dphansti
▴ 10 • written 10.0 years ago by
Dimitris Polychronopoulos
▴ 80
0
votes
1
reply
1.3k
views
Sushi example data not correct?
Sushi
updated 9.8 years ago by
dphansti
▴ 10 • written 9.8 years ago by
Till
▴ 30
0
votes
2
replies
1.7k
views
Error: no slot of name "start" for this object of class "XStringViews"
XStringViews
biostrings
9.9 years ago • updated 9.8 years ago
jbtouching
• 0
0
votes
2
replies
5.4k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2
rnaseq
plotMA
deseq
rna-seq
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
sjs0282
• 0
0
votes
2
replies
1.8k
views
How to set a negative coverage to ZERO
genomicranges
coverage
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
vanhzh
• 0
3
votes
2
replies
3.1k
views
How to represent a relationship between physical map and linkage map of a sequenced data using OmicCircos or another similar
omiccircos
software R
bioconductor for genomic data science
linkage disequilibrium
updated 9.8 years ago by
Hu, Ying NIH/NCI [E]
▴ 50 • written 9.8 years ago by
pertille
• 0
0
votes
1
reply
1.3k
views
Error ,when I use "pa.calls" function on my dataset
panp
Combat
9.8 years ago
Shamim Sarhadi
▴ 20
2
votes
3
replies
2.4k
views
visualing pwm motif on a DNAstring
pwmenrich
dnastringset
updated 9.8 years ago by
Robert Stojnic
▴ 50 • written 9.8 years ago by
sekawaiwai2006
▴ 20
0
votes
3
replies
2.0k
views
Calculating a score from fold change matrix of pair-wise rna-seq data
rna-seq
deseq2
differential gene expression
biostatistics
9.8 years ago
g.atla
▴ 10
2
votes
5
replies
2.5k
views
How to make sense of the fold change values in the interaction results object.
deseq2
logfoldchange
interactions
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
colaneri
▴ 30
1
vote
16
replies
3.2k
views
BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers on localhost
biocparallel
updated 9.8 years ago by
Martin Morgan
25k • written 9.9 years ago by
lee.tibbert
▴ 20
38
votes
23
replies
18k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
11.4 years ago • updated 10 months ago
Michael Love
43k
3
votes
13
replies
2.9k
views
Covariates in DESeq2 for Polysome profiling Data
deseq2
updated 9.8 years ago by
marco.trizzino83
▴ 10 • written 9.9 years ago by
c.oertlin
• 0
46,730 results • Page
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Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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