1
vote
2
replies
2.1k
views
Error with untar2 that blocks the installation of GO.db on Windows (R 3.5, Bioc 3.8) for using clusterProfiler
go.db clusterprofiler
updated 7.1 years ago by 25k • written 7.1 years ago by ★ 1.1k
2
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4
replies
3.1k
views
Filtering, minimum sample number, and condition in edgeR
edger filtering
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 30
1
vote
0
replies
992
views
create null sequences with gkmSVM for mouse genome mm10
gkmSVM
7.1 years ago fusion.slope ▴ 10
5
votes
2
replies
2.2k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
3
replies
1.6k
views
How to clear a cached S4 method
devtools S4 methods cache
7.1 years ago Michael Steinbaugh ▴ 90
0
votes
6
replies
2.3k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 7.1 years ago by ▴ 30 • written 7.1 years ago by • 0
1
vote
1
reply
1.2k
views
Calling a package specific function in a for loop
drimseq swimming downstream for loop sapply
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
1
vote
2
replies
1.4k
views
Comparing more than 2 experimental groups with MEDIPS?
medips medip-seq dna methylation dmr analysis
updated 7.1 years ago by ▴ 570 • written 7.1 years ago by • 0
2
votes
4
replies
2.2k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 60
3
votes
4
replies
2.7k
views
Error: 'biocValid' is not an exported object from 'namespace:BiocManager'
biocmanager
updated 7.1 years ago by 4.2k • written 7.1 years ago by • 0
0
votes
2
replies
1.6k
views
Rsubread installation failed
r package installation
7.1 years ago justinkablan225 ▴ 10
0
votes
2
replies
1.7k
views
feature reduction using machine learning
rnaseq machine learning feature selection
updated 7.1 years ago by ▴ 420 • written 7.1 years ago by • 0
0
votes
1
reply
1.5k
views
Pick coding vs non-coding from Ensembl data set
R ensembl ensembldb noncoding rna protein coding
updated 7.1 years ago by ★ 2.1k • written 7.1 years ago by • 0
1
vote
5
replies
1.6k
views
Biomart cannot get multiple genes?
R biomart
7.1 years ago Mike ▴ 10
2
votes
2
replies
2.5k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 10
8
votes
2
replies
1.8k
views
News: BioCAsia, 29-30th November 2018, Melbourne, Australia
news conference training News
updated 7.1 years ago by 53k • written 7.3 years ago by ▴ 170
0
votes
2
replies
1.8k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
7.1 years ago cschot3 • 0
1
vote
4
replies
1.9k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 2.7 years ago by 53k • written 7.1 years ago by ▴ 10
12
votes
4
replies
5.2k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by ▴ 30
2
votes
3
replies
2.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 30
0
votes
4
replies
2.7k
views
DESeq2 for Cut&Run and differential enrichment testing
deseq2 Cut&Run
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
2
replies
1.3k
views
getting the sequences of 3UTR and the gene names
GenomeFeatures
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 670
2
votes
6
replies
2.7k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
2
replies
1.5k
views
logfold shrinkage DESeq2
deseq2
7.1 years ago sherajilir • 0
0
votes
0
replies
1.2k
views
How to left or right align titles in Gviz tracks?
gviz title text formatting grid
7.1 years ago alex.gos90 ▴ 10
0
votes
1
reply
1.9k
views
DESeq2 paired design with missing samples and multiple conditions
deseq2 paired samples missing data multiple treatments
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
1
reply
1.7k
views
rtracklayer::Problem with export.bw of GRanges object created by unlisted after liftover from mm9 to mm10 of wig file
rtracklayer export.bw liftover
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 20
0
votes
2
replies
1.9k
views
MA plot scattering pattern
deseq2 MAplot
7.1 years ago avitalwasser • 0
0
votes
3
replies
1.3k
views
What does component or SCX classification in iTRAQ/TMT experiment represent?
proteomics
updated 7.1 years ago by 1.6k • written 7.1 years ago by • 0
0
votes
0
replies
1.3k
views
Query based on PMIDs
SRAdb geoquery
7.1 years ago Deepak Tanwar ▴ 10
1
vote
0
replies
1.5k
views
Job: CRUK Cambridge Centre MRes + PhD in Cancer Biology (Cross-Programme Quantitative Projects)
PhD cancer deep learning computational biology Job
7.1 years ago Shamith.Samarajiwa ▴ 180
3
votes
6
replies
3.5k
views
biomaRt: Ensembl -> Entrez conversion error?
biomart entrez gene identifiers ensembl conversion
updated 7.1 years ago by ★ 6.6k • written 7.1 years ago by ▴ 10
1
vote
1
reply
578
views
Do I have too many samples or are some samples causing issues?
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
7
replies
2.0k
views
A problem with csaw that I don't think is a problem with csaw
csaw caught segfault
7.1 years ago sorjuelal • 0
6
votes
7
replies
2.7k
views
Normalization for small non-coding RNA
TMM deseq2 smallrna rnaseq
updated 7.1 years ago by ▴ 510 • written 7.1 years ago by ▴ 90
6
votes
4
replies
2.8k
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 30
1
vote
0
replies
1.3k
views
Job: applied methods development for single-cell sequencing
single-cell job computational biology Job
7.1 years ago Simon Anders ★ 3.8k
1
vote
2
replies
3.6k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by • 0
0
votes
5
replies
1.4k
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 7.1 years ago by 68k • written 7.1 years ago by ★ 1.6k
0
votes
1
reply
1.5k
views
A recent update to readr cause issues loading data with GEOquery 2.50.0
version compatibility bug
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
0
votes
1
reply
764
views
DESeq2 on mixed species samples
deseq2
updated 7.1 years ago by 68k • written 7.1 years ago by ★ 1.4k
0
votes
1
reply
1.3k
views
Error when install bioconductor on Mac 10.12 Sierra
installation
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
14
votes
10
replies
4.9k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
7.1 years ago Deleted ▴ 70
1
vote
1
reply
3.8k
views
Question regarding class imbalance and low sample size for DESeq2
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
4
replies
1.8k
views
DESeq2 multifactor formula design
deseq2 time series multiple factor design
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
2
replies
1.8k
views
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2 design and contrast matrix
7.1 years ago bruce.moran ▴ 30
0
votes
0
replies
1.3k
views
ASpli Package: Problem with readCounts() function, no Junctions analysed.
rnaseq alternative splicing ASpli
7.1 years ago nicolas.guyon2 • 0
1
vote
2
replies
1.1k
views
DESeq2 - assessing expression of low count genes
deseq2 HERVs low counts prefiltering dispersion estimates
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 40
0
votes
2
replies
3.7k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
1
reply
981
views
DESeq2 ratio of small p-values plot
deseq2 diagnostic plots
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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