7
votes
7
replies
6.3k
views
convert S4 DataFrame of Rle objects to sparse matrix
s4
updated 10.7 years ago by ★ 11k • written 10.7 years ago by ▴ 180
4
votes
8
replies
3.4k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 10.7 years ago by 53k • written 10.7 years ago by ▴ 10
9
votes
20
replies
3.9k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 10.7 years ago by ★ 1.1k • written 10.8 years ago by ▴ 40
17
votes
4
replies
19k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.7 years ago by ▴ 30 • written 11.1 years ago by ▴ 680
0
votes
1
reply
3.6k
views
Array Express HuGene-1_1-st-v1 CDF problem
cdf microarray affy
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
0
votes
3
replies
1.4k
views
Getting annotated and normalized data.
microarray rstudio annotation
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
1
vote
2
replies
1.9k
views
error in sourcing biocLite: Error in get(".BioC_version_associated_with_R_version", envir = asNamespace("tools")
bioclite
10.7 years ago melanie.shook • 0
4
votes
1
reply
2.9k
views
Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 10.7 years ago by 25k • written 10.7 years ago by ▴ 10
2
votes
6
replies
2.9k
views
SICER and Diffbind
Sicer diffbind
10.8 years ago • updated 10.7 years ago sergio.espeso-gil • 0
1
vote
9
replies
3.3k
views
errors in namespaceExports during biocLite installs
biocinstaller installation
10.7 years ago shabbychef • 0
0
votes
2
replies
4.9k
views
package ‘ComplexHeatmap’ is not available
software error package
updated 10.7 years ago by ★ 1.2k • written 10.7 years ago by • 0
4
votes
2
replies
4.2k
views
PCA for voom normalized RNAseq data
voom pca
updated 10.7 years ago by ★ 29k • written 10.7 years ago by ▴ 120
1
vote
1
reply
1.6k
views
gviz: error when plotting BiomartGeneRegionTrack with just.group="above"
gviz
updated 10.7 years ago by ▴ 750 • written 10.7 years ago by ▴ 80
0
votes
3
replies
3.9k
views
DMRcate: incorporating covariates to find DMRs in methylation data?
limma illimina 450k methylation DMRcate
updated 10.7 years ago by ▴ 230 • written 10.7 years ago by ▴ 120
1
vote
5
replies
6.5k
views
HOPACH error: "negative length vectors are not allowed" in distancematrix(). Matrix too large?
hopach
updated 10.7 years ago by ▴ 110 • written 10.7 years ago by • 0
1
vote
13
replies
6.5k
views
'Codetools' and 'mgcv' packages fail to update
package updates codetools deseq mgcv
updated 10.7 years ago by • 0 • written 10.8 years ago by • 0
7
votes
4
replies
3.4k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 10.7 years ago by 53k • written 10.7 years ago by ▴ 10
1
vote
3
replies
2.1k
views
Genome side annotation for drosophila
genome annotation drosophila melanogaster org.Mm.eg.db
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 20
0
votes
1
reply
1.8k
views
CRSIPRseek: no summary file generated
GUI GUI
updated 10.7 years ago by ▴ 40 • written 11.4 years ago by ★ 4.3k
1
vote
6
replies
4.8k
views
DESeq 2, interaction model design
deseq2
10.7 years ago agbioinformatics • 0
1
vote
11
replies
2.7k
views
Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
dm2 bsgenome noncoding RNA
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 20
0
votes
0
replies
1.1k
views
cummeRbund :: filter on repFpkm
cummerbund repFpkm
10.7 years ago s.ghignone ▴ 10
0
votes
0
replies
1.3k
views
Invitation Research Collaborations
cancer microarray mirna sequencing
10.7 years ago alexandru.floares • 0
1
vote
2
replies
1.7k
views
Gene set analysis with CAMERA with interaction effect
gene set analysis
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
3
votes
7
replies
2.6k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 30
1
vote
5
replies
1.7k
views
how to test for genes of interest?
Normalization limma
updated 10.7 years ago by 53k • written 17.4 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
Background correction and normalization for very small customized arrays
Normalization background correction
updated 10.7 years ago by 53k • written 18.2 years ago by ▴ 60
0
votes
1
reply
1.6k
views
arrayQuality: error from maQualityPlots
arrayQuality
updated 10.7 years ago by 53k • written 18.8 years ago by ▴ 60
1
vote
1
reply
1.1k
views
limma: get list of genes after classifyTestsF
limma classifyTestsF
updated 10.7 years ago by 53k • written 18.9 years ago by ▴ 60
1
vote
2
replies
3.2k
views
extract info from limma results
limma
updated 10.7 years ago by 53k • written 18.9 years ago by ▴ 60
0
votes
1
reply
1.8k
views
Nested Comparison using DESeq2
deseq2 rnaseq
updated 10.7 years ago by ★ 7.9k • written 10.7 years ago by ▴ 60
4
votes
7
replies
3.4k
views
Diffbind dba.analyze Error in d$span : $ operator is invalid for atomic vectors
diffbind
updated 2.8 years ago by • 0 • written 10.8 years ago by ▴ 10
0
votes
0
replies
1.7k
views
openCyto transitional gate
flow cytometry opencyto
10.7 years ago Jiang, Mike ★ 1.3k
1
vote
1
reply
1.5k
views
error in installing genefilter package
software error
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
1
vote
3
replies
4.0k
views
gviz: name of tracks disappeas
gviz
updated 10.7 years ago by ★ 1.6k • written 10.7 years ago by ▴ 80
0
votes
1
reply
1.7k
views
gviz: BiomartGeneRegionTrack throws an error
gviz biomart
updated 10.7 years ago by ★ 1.6k • written 10.7 years ago by ▴ 80
1
vote
3
replies
2.6k
views
Gviz and older ENSEMBL biomarts
gviz biomart
updated 10.7 years ago by ★ 1.6k • written 11.2 years ago by • 0
0
votes
2
replies
1.4k
views
DEXSeq exon usage at sample level
dexseq exon usage
updated 10.7 years ago by ★ 1.9k • written 10.7 years ago by ▴ 10
0
votes
0
replies
1.0k
views
expression data filter of iClusterPlus
iClusterPlus variance filter
10.7 years ago zhouxiuqing • 0
3
votes
10
replies
5.8k
views
Getting a list of all tRNA encoding genes for an organism?
trna ncrna genomicfeatures featuredb biomart
updated 10.7 years ago by 16k • written 10.8 years ago by ▴ 180
5
votes
3
replies
2.8k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
10.9 years ago • updated 10.7 years ago Thomas Girke ★ 1.7k
0
votes
1
reply
1.7k
views
install xps in ubuntu 14.04
xps microarray installation
updated 10.7 years ago by ★ 3.9k • written 10.7 years ago by • 0
1
vote
1
reply
2.3k
views
Does manual pre-filtering of the data on read counts violate the assumptions of the dispersion estimation in DESeq2?
deseq2 pre-filtering
updated 10.7 years ago by 43k • written 10.7 years ago by ★ 2.1k
0
votes
6
replies
7.4k
views
DESEq2: Two factor design without interaction
deseq2
updated 3.8 years ago by ▴ 60 • written 10.7 years ago by • 0
2
votes
2
replies
2.2k
views
floating toc with BiocStyle
BiocStyle
updated 10.7 years ago by ▴ 750 • written 10.7 years ago by ★ 1.2k
0
votes
1
reply
3.2k
views
plotMA in DEseq2
DEseq2
updated 10.7 years ago by 43k • written 10.7 years ago by ▴ 50
0
votes
0
replies
1.1k
views
Bumphunter Output Details
bumphunter
10.7 years ago andrew.j.skelton73 ▴ 370
0
votes
3
replies
2.2k
views
Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
10.8 years ago • updated 10.7 years ago Cheng-Yuan Kao ▴ 100
0
votes
4
replies
1.6k
views
Rsamtools failing to parse PEDIGREE header
Rsamtools
updated 10.7 years ago by ★ 6.8k • written 10.7 years ago by • 0
0
votes
4
replies
18k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 10.7 years ago by 43k • written 10.7 years ago by ▴ 60
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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