0
votes
1
reply
1.5k
views
specify the color in plotMutationSpectrum() of SomaticSignatures library
SomaticSignatures
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by ▴ 100
0
votes
1
reply
2.0k
views
Errors installing RforProteomics
Bioc package installation rforproteomics
updated 9.9 years ago by 1.6k • written 9.9 years ago by • 0
0
votes
2
replies
1.6k
views
Error viewing the data set Golub_Merge
golubEsets rstudio
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
6
votes
10
replies
6.6k
views
DESEQ2--compare two log2-transformed fold changes
deseq2 compare two log2-transformated fold changes
9.9 years ago an.anand233 ▴ 30
0
votes
3
replies
1.5k
views
cellHTS2 configure error
cellHTS2
updated 9.9 years ago by ▴ 160 • written 9.9 years ago by • 0
0
votes
1
reply
1.6k
views
FlowViz package question
flowviz flowcytometry
9.9 years ago Jiang, Mike ★ 1.3k
0
votes
1
reply
916
views
DiffBind with 21 contrast???
diffbind
updated 9.9 years ago by ★ 5.2k • written 9.9 years ago by • 0
2
votes
2
replies
7.4k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 10
0
votes
11
replies
6.2k
views
Examples from keggList in KEGGREST don't all work
software error keggrest
9.9 years ago Bryan Hanson • 0
2
votes
2
replies
1.8k
views
How to rename seqlevels style (I, II, III, ...,XVI, Mito to 1,2,3,...16, 17.) in txdb granges?
renameSeqlevels mapSeqlevels grangeslist granges txdb
9.9 years ago vinod.acear ▴ 50
0
votes
1
reply
1.2k
views
How to post a job
Post Doctorate Job
updated 9.9 years ago by 25k • written 9.9 years ago by • 0
0
votes
0
replies
1.8k
views
Goseq package in R:getting terms after using getgo
R bioconductor gene ontology
9.9 years ago javier.mendoza • 0
0
votes
0
replies
1.0k
views
Methylpipe function pool.reads gives syntax error
methylpipe
9.9 years ago pirona • 0
0
votes
4
replies
2.2k
views
danRer10 is missing in geneLenDataBase
genelendatabase goseq
updated 9.9 years ago by ▴ 320 • written 9.9 years ago by • 0
20
votes
10
replies
9.0k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 180
1
vote
2
replies
1.5k
views
CRISPRseek searching requirement
CRISPRSEEK
updated 9.9 years ago by ★ 4.3k • written 9.9 years ago by • 0
0
votes
3
replies
12k
views
Weird error in the package submission
software error
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by ▴ 10
0
votes
5
replies
1.9k
views
AnnotationHub() returns only one record !?
annotationhub
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by • 0
0
votes
0
replies
1.4k
views
customproDB: gene fusions
fusion bed files gene fusion bed file
9.9 years ago ramaniak • 0
3
votes
4
replies
1.5k
views
bounded trended dispersion edgeR
edger
updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 180
0
votes
1
reply
693
views
Gene expression data normalization by family pedigree
oligo
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
0
votes
1
reply
1.2k
views
Really weird results when I filter this new data that I have, script has worked on two previous data sets.
microarray limma genefilter
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
0
votes
0
replies
970
views
bug: open(FaFile(file)) segfaults with a 'memory not mapped' if file happens to be a directory
software error
9.9 years ago Philip Lijnzaad ▴ 160
1
vote
0
replies
1.6k
views
visualizing top differentially spliced genes
limma voom alternative splicing
9.9 years ago osa.zuta ▴ 40
0
votes
2
replies
1.5k
views
a naive question about aov() in R
R
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 40
2
votes
3
replies
9.9k
views
Adding text labels to PCA plot
deseq2
9.9 years ago John ▴ 30
0
votes
1
reply
1.8k
views
DESeq's estimateDispersions does not work
error in glm.fit
updated 9.9 years ago by ★ 13k • written 9.9 years ago by • 0
2
votes
7
replies
3.2k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
9.9 years ago tmartinez • 0
2
votes
4
replies
3.8k
views
Arguments for camera (gene set analysis)
camera GSEA
updated 9.9 years ago by ★ 13k • written 9.9 years ago by ▴ 10
5
votes
16
replies
3.8k
views
Read counts generated by SGSeq are always 0
sgseq splicing alternative splicing
updated 9.9 years ago by ▴ 260 • written 9.9 years ago by ▴ 20
0
votes
4
replies
2.2k
views
Error in parseURI("") : cannot parse URI (rtracklayer package)
rtracklayer
9.9 years ago Qiang ▴ 80
1
vote
5
replies
2.2k
views
Error: Number of PMs or MMs is zero (xps package)
rlm plm rnadegradationplot xps
updated 9.9 years ago by ★ 3.9k • written 9.9 years ago by ▴ 120
0
votes
1
reply
3.5k
views
DESeq2 releveling not changing resultsNames options
deseq2 relevel resultsNames multifactorial design
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 20
0
votes
1
reply
1.7k
views
Subsetting the geno fields in a VCF using VariantAnnotation
VariantAnnotation
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 110
1
vote
1
reply
1.7k
views
flowDensity, nmRemove and xyplot
flowdensity flowviz
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by ▴ 30
0
votes
4
replies
1.9k
views
is it possible to create this comparison?
rnaseq pairwise multiple comparisons deseq2
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
2
votes
0
replies
1.8k
views
News: Course: Analysis of RNA-seq and ChIP-seq data, March 29th - April 1st, Oeiras, Portugal
Course workshop News
9.9 years ago Mark Dunning ★ 1.1k
0
votes
1
reply
1.7k
views
Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
gviz ucsc
updated 9.9 years ago by ▴ 750 • written 9.9 years ago by • 0
2
votes
7
replies
9.8k
views
heatmap log2foldchange values
deseq2
9.9 years ago John ▴ 30
3
votes
3
replies
6.0k
views
Run featureCounts in isoform/transcript level in Rsubread
rsubread
updated 9.9 years ago by ★ 3.6k • written 9.9 years ago by ▴ 40
0
votes
1
reply
1.5k
views
FlowMerge: Get Count, Frequencies, MFI from resulting cluster
flowmerge MFI
updated 9.9 years ago by ▴ 240 • written 10.2 years ago by • 0
4
votes
3
replies
3.5k
views
Is there an R package providing an R API for IGV / igvtools out there?
package IGV
updated 9.9 years ago by ▴ 470 • written 9.9 years ago by ★ 2.4k
2
votes
5
replies
4.8k
views
A parser for Tiled Data File (TDF) format?
file format parser IO TDF IGV
9.9 years ago Henrik Bengtsson ★ 2.4k
2
votes
2
replies
1.9k
views
SGSeq: class of "sample_info" argument of analyzeFeatures, data.frame or DataFrame!
sgseq
updated 9.9 years ago by ▴ 260 • written 9.9 years ago by ▴ 40
1
vote
3
replies
25k
views
Converting first column to rownames
rstudio
9.9 years ago John ▴ 30
0
votes
0
replies
1.2k
views
Help with loading Data and reading Ct values
htqpcr
9.9 years ago Pheebz • 0
0
votes
0
replies
1.5k
views
Defining metagenes from NMF in methylation array data - next step?
NMF minfi
9.9 years ago yura.grabovska ▴ 30
0
votes
4
replies
1.9k
views
error in import.exon.scheme, XPS package
xps import.exon.scheme error rnadegradationplot
9.9 years ago Biologist ▴ 120
0
votes
2
replies
1.7k
views
ENCODExplorer update snapshot: 404 error
encodexplorer
9.9 years ago liz.ingsimmons ▴ 140
3
votes
6
replies
2.9k
views
List of package names with versions
packages
updated 9.9 years ago by • 0 • written 9.9 years ago by • 0
46,719 results • Page 408 of 935
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Replies
Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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