6
votes
5
replies
2.1k
views
Pigengene : BN network using consensus module
Pigengene
updated 7.1 years ago by ▴ 200 • written 7.2 years ago by ▴ 10
1
vote
1
reply
959
views
Bug report for GenomicRanges
genomicranges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 170
1
vote
4
replies
1.9k
views
IHW multiple testing correction
IHW multiple testing correction covariate distribution
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
4
votes
8
replies
50k
views
What is colData? How do I make one?
deseq2 coldata
updated 7.1 years ago by ★ 1.4k • written 7.1 years ago by ▴ 10
1
vote
1
reply
876
views
DESeq2 namespace load fail
deseq2
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
1
vote
1
reply
1.5k
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
7.1 years ago Sebastian Hesse ▴ 70
0
votes
0
replies
877
views
Job: RNA Computational Biologist at Panorama Medicine in Philadelphia
rna-seq Job
7.1 years ago Jeremy Leipzig ▴ 70
0
votes
2
replies
1.5k
views
trouble with installing "affyio"
affyio rstudio docker R 3.5.0
7.1 years ago shidaxia • 0
3
votes
3
replies
1.7k
views
How to decide whether a variate should be in the model or not
deseq2 rnaseq
updated 2.8 years ago by 43k • written 7.1 years ago by ▴ 20
0
votes
2
replies
1.1k
views
Getting an error trying to do tximportData tutorial
deseq2 tximport
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
5
votes
8
replies
1.8k
views
High normalized counts on DESeq2 MAplot
deseq2 maplot
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 60
1
vote
4
replies
1.1k
views
importing Tximport to DESeq2 for a time series experiment
deseq2 tximport
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
vote
4
replies
1.8k
views
UniProt.ws non-functional or abandoned?
uniprot.ws uniprot uniprot accessions
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
0
replies
674
views
Converting DESeq2 results to DiffBind object
deseq2 diffbind
7.1 years ago rbronste ▴ 60
1
vote
6
replies
1.3k
views
what is the correct command line to import my txi data file as a deseq2 dataset in a time series experiment
deseq2
7.1 years ago ahmedaalkarim • 0
2
votes
4
replies
2.1k
views
Split GRanges to GRangeList based on mcols value
granges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
votes
1
reply
907
views
Using Wald test after lfcShrink (dds, contrast ())
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
vote
9
replies
2.4k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ★ 1.5k
1
vote
1
reply
876
views
DESeq2/apeglm s-values: Why average FSR (or FSOS) instead of maximum?
DESeq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
1
reply
1.6k
views
Error in .merge_transcript_parts(transcripts)
maketxdbfromgff
7.1 years ago csijcs • 0
0
votes
2
replies
1.6k
views
create.set on MEDIPS
medips createset
updated 7.1 years ago by ▴ 570 • written 7.1 years ago by • 0
1
vote
1
reply
666
views
Differential expression where only certain samples are paired
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
1
vote
3
replies
1.9k
views
masigpro: could not find function "negative.binomial"
masigpro
7.1 years ago nicolas.descostes ▴ 20
2
votes
2
replies
4.0k
views
How to access gene IDs associated with GO terms in GOSeq
GOseq ensemblid GO
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
1
reply
1.1k
views
Functions listFilterValues and searchFilterValues are not working in biomaRt
biomart
updated 7.1 years ago by ★ 6.6k • written 7.1 years ago by • 0
0
votes
1
reply
3.8k
views
Different results come from GO enrichment analysis with ENSEMBL ID and ENTREZID as keyTypes
clusterprofiler go enrichment functional enrichment
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by ▴ 20
4
votes
4
replies
4.8k
views
Why does DEseq2 take a long time to run on large dataset ?
DEseq2 large dataset
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
votes
0
replies
1.2k
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
7.1 years ago lkianmehr • 0
0
votes
0
replies
1.2k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
7.1 years ago A ▴ 60
0
votes
0
replies
1.1k
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
7.1 years ago saripalligautam86 ▴ 10
3
votes
9
replies
6.8k
views
topGO "invalid argument to unary operator"
software error topgo
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
0
replies
855
views
split champ.load for large number of samples
memory problem champ.load
7.1 years ago petra.lenzini • 0
4
votes
7
replies
3.2k
views
Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
deseq2 design model rnaseq multiple factor levels
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
vote
6
replies
12k
views
Cannot install Bioconductor Packages. Cannot install BiocManager.
software error bioconductor biocmanager
updated 7.1 years ago by 4.2k • written 7.2 years ago by ▴ 10
2
votes
2
replies
2.8k
views
dba.count Can't count: some peaksets are not associated with a .bam file.
diffbind
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by • 0
0
votes
1
reply
830
views
DESeq2 multiple treatments
deseq2
7.1 years ago preetomregon • 0
0
votes
0
replies
1.5k
views
Job: PhD and PostDoc position in computational cancer biology in Milan
bioinformatician job bioinformatics scientist cancer genomics biostatistics network analysis Job
7.1 years ago marschaefer • 0
0
votes
0
replies
1.5k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
7.1 years ago Mithil Gaikwad • 0
2
votes
2
replies
1.7k
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
7.1 years ago 2323982403 ▴ 60
3
votes
3
replies
3.3k
views
Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
edgeR prior.count
updated 7.1 years ago by 53k • written 7.1 years ago by ★ 2.0k
0
votes
2
replies
1.6k
views
Biostrings install error
biostrings install error
7.1 years ago owenchapman1 • 0
3
votes
8
replies
2.5k
views
FourCSeq - how to write tables with the results
fourcseq
updated 7.1 years ago by • 0 • written 10.2 years ago by • 0
0
votes
2
replies
1.2k
views
Deseq2 paired analysis
deseq2 paired samples interaction terms
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
1
reply
1.9k
views
mzR Error (different Version)
mzr metab
updated 7.1 years ago by 1.6k • written 7.1 years ago by • 0
0
votes
1
reply
700
views
DESeq2 with 3 treatment +3 genotype
deseq2
7.1 years ago hussienfotoh • 0
0
votes
2
replies
1.3k
views
Memory usage and SWATH2stats
swath dia msstats swath2stats
updated 7.1 years ago by • 0 • written 7.1 years ago by • 0
0
votes
7
replies
1.2k
views
Differential Expression - DESeq2 identifies to many differentially expressed genes (~20,000)
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
6
votes
7
replies
3.4k
views
bplapply with progressbar
bplapply progressbar
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
0
votes
0
replies
1.1k
views
draw.pairwise.venn: Misplaced line connecting external area label
venndiagram
7.1 years ago salamandra ▴ 20
1
vote
6
replies
3.2k
views
Recommended way to use BiocInstaller / BiocManager in packages on CRAN?
cran biocinstaller biocmanager
updated 7.1 years ago by 25k • written 7.2 years ago by ▴ 130
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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