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4.4k
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Dealing with the output of ssGSEA method from GSVA package
gsva
ssgsea
10.2 years ago
Momeneh Foroutan
▴ 10
0
votes
0
replies
1.8k
views
Job:
Senior Bioinformatics Researcher - University of Adelaide, South Australia
bioinformatician job
australia
veterinary science
c++
java
Job
10.2 years ago
Steve Pederson
▴ 170
0
votes
1
reply
1.8k
views
Extract methylation data from a FirehoseData
RTCGAToolbox
updated 10.2 years ago by
samur
• 0 • written 10.2 years ago by
carlos.ruiz
• 0
0
votes
0
replies
1.3k
views
RADseq chromosomes unknown
snprelate
RADseq
Stacks
10.2 years ago
clive.darwell
• 0
0
votes
3
replies
1.6k
views
I want to sample (random ) nucleic acids at middle 20 positions of DNAstring set
DNAStringSet
sample
updated 10.2 years ago by
Hervé Pagès
16k • written 10.2 years ago by
vinod.acear
▴ 50
1
vote
3
replies
1.6k
views
saving raw interaction matrices using diffHic
diffhic
interaction matrix
10.2 years ago
roladali
▴ 20
0
votes
5
replies
2.1k
views
Mapping short reads to gene IDs in GPL9115
rnaseq
EST
gene Id
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
NS
▴ 60
0
votes
3
replies
1.6k
views
Sampling protein coding genes of the same length distribution as another set of elements using GRanges
granges
R
sample
updated 10.2 years ago by
Julian Gehring
★ 1.3k • written 10.2 years ago by
Dimitris Polychronopoulos
▴ 80
0
votes
3
replies
2.7k
views
problem with WGCNA
geneexpression
updated 10.2 years ago by
Peter Langfelder
★ 3.0k • written 10.2 years ago by
nazaninhoseinkhan
• 0
3
votes
9
replies
5.4k
views
Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
microarray
normalization
oligo
updated 10.2 years ago by
burchard
• 0 • written 11.2 years ago by
tangboyun
▴ 30
2
votes
8
replies
2.3k
views
Problem fetching resources from AnnotationHub, error 403
AnnotationHub
updated 10.2 years ago by
Valerie Obenchain
★ 6.8k • written 10.2 years ago by
Johannes Rainer
★ 2.1k
11
votes
1
reply
19k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 10.2 years ago by
Michael Love
43k • written 10.2 years ago by
tony_cybercloud
▴ 20
0
votes
1
reply
2.4k
views
Invalid vertex id while running R_igraph_spinglass_my_community on FEM package
FEM
igraph
updated 10.2 years ago by
andrew
• 0 • written 10.2 years ago by
sirintra
▴ 10
2
votes
1
reply
3.7k
views
Installation of bioConductor packages
installation
packages
bioconductor
all
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
av
• 0
0
votes
3
replies
3.7k
views
error in vsn package
vsn
failure to read documentation error
updated 10.2 years ago by
Wolfgang Huber
★ 13k • written 10.2 years ago by
Angel
▴ 40
2
votes
1
reply
2.0k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina
bioconductor
limma
microarray
normalization
updated 10.2 years ago by
Gordon Smyth
53k • written 10.2 years ago by
Konstantinos Yeles
▴ 90
3
votes
8
replies
31k
views
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
BiocUpgrade
Rstudio
Bioconductor
R3.2.2
10.2 years ago
svlachavas
▴ 840
0
votes
0
replies
1.2k
views
problem of GOSemSim R package operation
R package problem
10.2 years ago
zjzace
• 0
0
votes
1
reply
1.2k
views
TDARACNE:::ToTheGraph_timeShiftmax2 doesn't support more than 1000 edges
software error
tdaracne
updated 10.2 years ago by
zoppoli pietro
▴ 10 • written 10.2 years ago by
sergisayolspuig
▴ 80
0
votes
3
replies
1.8k
views
ChIPpeakAnno (makeVennDiagram) giving different results than before
chippeakanno
venn diagram
updated 10.2 years ago by
Ou, Jianhong
★ 1.3k • written 10.2 years ago by
R.A. Tomaz
• 0
0
votes
1
reply
1.7k
views
phyloseq - plot_bar() error
phyloseq
plot_bar()
updated 10.2 years ago by
mcmurdie
▴ 20 • written 10.2 years ago by
Brian Smith
▴ 120
2
votes
5
replies
3.2k
views
Plot data from VCF using Gviz?
gviz
variantannotation
vcf
updated 10.2 years ago by
Valerie Obenchain
★ 6.8k • written 10.2 years ago by
Johannes Rainer
★ 2.1k
1
vote
7
replies
3.1k
views
Error message from updated DESeq2
deseq2
beta prior
error
10.2 years ago
asaferali
• 0
1
vote
1
reply
1.6k
views
metagenomeSeq - normFactors
metagenomeseq
updated 10.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 10.2 years ago by
Brian Smith
▴ 120
2
votes
12
replies
4.4k
views
Error: failed to load 'AnnotationHub' resource
biomart
annotationhub
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
borowczak.marc
▴ 10
1
vote
1
reply
2.2k
views
Data handling in DESeq2
deseq2
data handling
comparing more than two groups
normalization
logfc
updated 10.2 years ago by
Michael Love
43k • written 10.2 years ago by
bioboy
• 0
0
votes
3
replies
1.6k
views
Question on DESeq2 nested model example
deseq2
design matrix
updated 10.2 years ago by
Michael Love
43k • written 10.2 years ago by
Guido Hooiveld
★ 4.1k
4
votes
3
replies
1.7k
views
SomaticSignatures : change order of x-axis in plotMutationSpectrum
somaticsignatures mutationcontext
updated 10.2 years ago by
Julian Gehring
★ 1.3k • written 10.2 years ago by
sergio.martinezcuesta
▴ 10
1
vote
2
replies
1.8k
views
read.FCS error on FCS import
flowcore
10.2 years ago
Kipper Fletez-Brant
▴ 150
0
votes
3
replies
2.3k
views
I want have a score vector of length of grange that is overlapping with other grange.
granges
findoverlaps
subsetbyoverlaps
updated 10.2 years ago by
Michael Lawrence
★ 11k • written 10.2 years ago by
vinod.acear
▴ 50
0
votes
3
replies
1.7k
views
Question on DESeq2 on concatenated factors model vs. full interaction model
deseq2
updated 10.2 years ago by
Simon Anders
★ 3.8k • written 10.2 years ago by
Dr Wei Chen
▴ 10
5
votes
6
replies
3.1k
views
Translating model formula from DESeq to DEXSeq
dexseq
linear model
formula
updated 10.2 years ago by
Alejandro Reyes
★ 1.9k • written 10.2 years ago by
Cornwell, Adam
▴ 110
0
votes
1
reply
2.1k
views
Plotting flow cytometry data
flowviz
flowcore
updated 10.2 years ago by
Jiang, Mike
★ 1.3k • written 10.2 years ago by
gori73
• 0
15
votes
2
replies
20k
views
Extract sequence from DNAStringSet object
dnastringset
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
komal.rathi
▴ 120
2
votes
3
replies
4.4k
views
BiocParallel example does not work any more (sbatch produced exit code 1)
biocparallel
slurm
updated 10.2 years ago by
Valerie Obenchain
★ 6.8k • written 10.2 years ago by
mertes
• 0
0
votes
4
replies
2.9k
views
Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this object of class 'GenomicMethylSet'"?
minfi
updated 10.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.2 years ago by
metamaden
▴ 10
0
votes
1
reply
2.4k
views
ERROR: dependency ‘pcalg’ is not available for package ‘miRLAB’
build/check error
updated 10.2 years ago by
brian.long
▴ 10 • written 10.2 years ago by
thucmi
• 0
0
votes
2
replies
2.0k
views
getting masked sequence from BSgenome: can I use Views or getSeq?
updated 10.2 years ago by
kielpinski
• 0 • written 13.2 years ago by
Janet Young
▴ 740
0
votes
0
replies
1.3k
views
maskedBSgenome - cannot enable masks
mask
bsgenome
10.2 years ago
kielpinski
• 0
7
votes
5
replies
4.5k
views
edgeR effects of design on testing main effects and interactions
edger
glmfit
glmlrt()
updated 10.2 years ago by
Aaron Lun
★ 29k • written 10.2 years ago by
cadeans
• 0
1
vote
6
replies
2.9k
views
Error: subsetting GenomicRanges with disjoint ranges produces errors
software error
genomicranges
10.2 years ago
ripkrizbi
• 0
3
votes
4
replies
2.8k
views
having trouble with dexseq_prepare_annotation.py
dexseq
gtf
updated 10.2 years ago by
Alejandro Reyes
★ 1.9k • written 10.2 years ago by
vakul.mohanty
▴ 20
1
vote
2
replies
7.1k
views
change the biomaRt host
biomaRt
updated 10.2 years ago by
hygine
▴ 140 • written 10.2 years ago by
Cheng-Yuan Kao
▴ 100
1
vote
2
replies
1.8k
views
Rsamtools pileup does not return reference base information
r
rsamtools
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
komal.rathi
▴ 120
1
vote
2
replies
3.0k
views
DESeq2 -- Comparing factors while fixing another factor
deseq2
differential gene expression
multiple factor design
updated 10.2 years ago by
Michael Love
43k • written 10.2 years ago by
David Eccles (gringer)
▴ 30
1
vote
2
replies
2.2k
views
AnnotationHub: change download location of database
annotationhub
installation
updated 10.2 years ago by
Martin Morgan
25k • written 10.2 years ago by
Guido Hooiveld
★ 4.1k
0
votes
4
replies
2.6k
views
Error running makeTxDbFromGFF
genomicfeatures
updated 10.2 years ago by
Keith Hughitt
▴ 180 • written 10.2 years ago by
jmmonroykuhn
• 0
6
votes
7
replies
6.4k
views
BiomaRt workaround when Biomart server closed
biomart
updated 10.2 years ago by
Sarai.Mola
• 0 • written 10.2 years ago by
s.corley
▴ 30
0
votes
1
reply
2.7k
views
non-numeric argument to binary operator error with makeBackground() in PWMEnrich
pwmenrich
MotifDB
updated 10.2 years ago by
Robert Stojnic
▴ 50 • written 10.2 years ago by
elliott77
• 0
1
vote
3
replies
2.0k
views
How to access error log from build report
build
testthat
cmd check
updated 10.2 years ago by
James W. MacDonald
68k • written 10.2 years ago by
Peter
• 0
46,730 results • Page
428 of 935
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Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Hugo Gruson
• 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat?
by
LillianaVolkman99
• 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa
by
Gordon Smyth
53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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