1
vote
4
replies
1.7k
views
Problem with Upgrade to Bioconductor 3.8 on Scientific linux (CentOS) 7
upgrade
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 10
0
votes
0
replies
1.4k
views
CAGEr get TSS in bed file
TSS promoter cage cager
7.1 years ago bharata1803 ▴ 60
6
votes
10
replies
4.7k
views
edgeR paired samples with blocking
limma edger blocking paired samples
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 10
2
votes
2
replies
1.6k
views
voom variance modeling: lowess curve fitting notation misunderstanding?
voom
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
0
votes
1
reply
1.5k
views
STRINGdb: enrichment function raises error
STRINGdb stringdb gene set enrichment analysis software error go
7.1 years ago wsciekly.maciek ▴ 10
4
votes
9
replies
4.1k
views
DESeq2 - Upgrade from 1.20.0 to 1.22.1 now gives warnings 'package:stats' may not be available when loading
deseq2
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 30
0
votes
3
replies
1.3k
views
Pairwise comparisons for "both between and within subject"experiment using DESeq2
pairwise deseq2 extracting contrasts resultsnames results deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
votes
1
reply
1.9k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 7.1 years ago by ▴ 290 • written 7.1 years ago by ▴ 10
0
votes
3
replies
2.9k
views
DESeq2: removal of duplicated genes during statistical analysis
deseq2 gene symbol ensembl
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
1
vote
1
reply
1.3k
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
votes
1
reply
2.7k
views
converting mstrg labels from stringtie and prepDE.py to gene symbol for downstream biology
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
4
votes
7
replies
2.0k
views
Are spurious correlations possible in correlating two DESeq2 foldchanges computed using the same reference sample group?
deseq2 correlation
7.1 years ago Cornwell, Adam ▴ 110
1
vote
1
reply
1.9k
views
annotatr: CpG Island/Shore/Shelf IDs
annotatr
updated 7.1 years ago by ▴ 140 • written 7.1 years ago by • 0
0
votes
0
replies
1.3k
views
Job: PhD Positions in Computational Cancer Research at the German Cancer Research Center (DKFZ) in Heidelberg
phd computer science computational biology bioinformatics phd position Job
7.1 years ago DKFZ International PhD Program ▴ 10
0
votes
1
reply
1.5k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
3
replies
5.6k
views
Rhdf5lib install problems
R bioconductor rhdf5 biocmanager 3.5
7.1 years ago cem45 • 0
3
votes
3
replies
2.5k
views
GZIP ERROR:-2 using featureCounts (Subread)
software error rnaseq
7.1 years ago gbreard ▴ 10
0
votes
0
replies
1.4k
views
Job: Postdoctoral position in applied bioinformatics - Milan
bioinformatician job epigenomics hts Job
7.1 years ago mattia pelizzola ▴ 200
0
votes
1
reply
3.8k
views
Timeout was reached error in GEOquery package
R microarray software error
updated 7.1 years ago by ★ 4.0k • written 7.1 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Job: Stipendium Hungaricum Fellowship with the Computational Biology Group of Semmelweis University
cancer genomics job budapest bioinformatics Job
7.1 years ago Endre Sebestyén ▴ 70
0
votes
0
replies
1.8k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
7.1 years ago kbobowik • 0
1
vote
2
replies
1.5k
views
covert from RGList to uRNAList
agilent agimicrorna
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 30
2
votes
1
reply
1.3k
views
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR design matrix contrast
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
1
vote
2
replies
1.3k
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
7.1 years ago Arman Shahrisa ▴ 20
0
votes
7
replies
3.0k
views
DEXSeqHTML getListElement GRanges error
dexseq software error bug
updated 7.1 years ago by ▴ 140 • written 7.1 years ago by • 0
0
votes
4
replies
1.5k
views
DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
7.1 years ago Maithê Barros ▴ 10
1
vote
5
replies
2.6k
views
edgeR: boxplot the expression of a gene in two conditions after glmFit
edgeR
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 10
1
vote
5
replies
1.8k
views
[DEVELOPMENT] Trying to use development version of Bioconductor, needs R 3.6?...
developers bioc-devel
7.1 years ago Casper van Mourik • 0
0
votes
1
reply
772
views
Issue with normalization in DESeq2
deseq2 normalization rnaseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
7
replies
1.9k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 100
3
votes
2
replies
1.6k
views
Error installing graphite
graphite
updated 7.1 years ago by ▴ 100 • written 7.1 years ago by ▴ 760
2
votes
6
replies
2.6k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 20
0
votes
5
replies
1.8k
views
Error in gmapR: gsnap not functioning
software error gmapr
updated 7.1 years ago by ★ 11k • written 7.1 years ago by • 0
0
votes
6
replies
1.6k
views
Another Matrix is not full rank question, multi-factor design issues
deseq2 model matrix not full rank multiple factor design
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
1
vote
2
replies
1.9k
views
Error in checkForRemoteErrors(val) : QuasR: can't pass alignment parameters
quasR quasr error alignmentparameters quasr
7.1 years ago Amer Ghalawinji • 0
0
votes
0
replies
1.1k
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Interpretation of PVCA result and what to correct for
pvca batch effect batch effect correction
7.1 years ago Sebastian Hesse ▴ 70
1
vote
1
reply
1.5k
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 7.1 years ago by ▴ 70 • written 7.1 years ago by ▴ 10
0
votes
2
replies
2.7k
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Please help with workspace error in R
R test fisher exact workspace
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 20
0
votes
1
reply
1.3k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 7.1 years ago by ★ 6.8k • written 7.1 years ago by ▴ 20
3
votes
19
replies
3.7k
views
EBImage computeFeatures error
ebimage image processing computefeatures
updated 7.1 years ago by ★ 6.6k • written 7.1 years ago by ▴ 20
0
votes
3
replies
1.3k
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Duplicate issue in ELMER get.pair for HNSC data
HNSC ELMER
7.1 years ago ghafarpour • 0
0
votes
7
replies
1.8k
views
Double nested design in DESeq2
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
4
replies
1.9k
views
tximport and its version
tximport stringtie RNA-seq analysis
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
6
votes
8
replies
4.0k
views
alpha in lfcshrink?
deseq2
updated 4.7 years ago by ▴ 80 • written 7.1 years ago by ▴ 20
0
votes
1
reply
1.4k
views
How to keep the genes whose counts are equal or greater than 10
deseq2 filtering
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
3
replies
1.1k
views
Pre-filtering results influence on downstream analysis
deseq2 rnaseq
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 20
0
votes
0
replies
618
views
adjustments in lfa
lfa
7.1 years ago minsuns • 0
2
votes
4
replies
3.1k
views
Problems installing RBGL in R
rbgl r package problem
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 20
2
votes
5
replies
1.7k
views
Error in get(cdfname, object 'mm430mmentrezgcdf' not found
affy cdf rma
updated 7.1 years ago by ★ 4.1k • written 7.1 years ago by • 0
0
votes
0
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problem with DeMAND, gene expression matrix input
DeMAND gene expression
7.1 years ago chipolino • 0
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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