1
vote
2
replies
2.2k
views
Display BrowseSeqs output in R Notebook?
BrowseSeqs DECIPHER notebook rmarkdown
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by • 0
0
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2
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1.5k
views
'GO_analyse' function error
goexpress ExpressionSet GO_analyse
6.4 years ago rezashiralmohammad • 0
1
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2
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1.5k
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 160
5
votes
14
replies
3.7k
views
Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
6.4 years ago Aditya ▴ 160
0
votes
1
reply
1.1k
views
I am wondering whether Gviz can plot thin box(noncoding part) directly from GRange
Gviz
updated 6.4 years ago by ▴ 750 • written 6.4 years ago by ▴ 40
2
votes
2
replies
2.8k
views
Filtering GFF3 file
annotation gff3 gff genome
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 10
0
votes
19
replies
3.6k
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Help with using CRISPRseeker
CRISPR
updated 6.4 years ago by ★ 4.3k • written 6.5 years ago by ▴ 40
0
votes
0
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1.2k
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News: R/Bioconductor for Mass Spectrometry and Proteomics course in Berlin
Bioconductor R News
6.4 years ago info ▴ 10
0
votes
5
replies
2.5k
views
ATACseqQC installation fails at shiny step
ATACseqQC
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
1
vote
3
replies
1.5k
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 6.4 years ago by 4.3k • written 6.5 years ago by ▴ 10
0
votes
3
replies
1.0k
views
SGSeq: core dumped after running convertToSGFeatures() method
sgseq coredump
6.4 years ago Sylvain Foisy ▴ 80
0
votes
5
replies
2.1k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 6.4 years ago by 1.6k • written 6.4 years ago by • 0
3
votes
2
replies
3.0k
views
How to arrange multiple Gviz plots into a multipanelfigure?
Gviz
updated 6.4 years ago by ▴ 750 • written 6.4 years ago by ▴ 160
0
votes
0
replies
749
views
REDSeq export data
Lihua Julie Zhu REDseq restriction enzymes
6.4 years ago pierre.reimbold • 0
0
votes
0
replies
904
views
massiR Extracting and Plotting Y Chr Probe Data
probe microarray
6.4 years ago Steve Lowe ▴ 30
5
votes
6
replies
2.0k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 6.4 years ago by ▴ 900 • written 6.4 years ago by ▴ 10
0
votes
1
reply
2.8k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
6.4 years ago Andrew_McDavid ▴ 280
0
votes
2
replies
2.5k
views
Obtaining recount project data in TPM?
recount
updated 6.4 years ago by ★ 1.1k • written 6.4 years ago by • 0
0
votes
2
replies
1.6k
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 6.4 years ago by ★ 1.9k • written 6.4 years ago by • 0
0
votes
1
reply
1.5k
views
News: List of Deprecated Packages Bioc 3.10
annotation experimentdata software deprecation release News
6.5 years ago • updated 6.4 years ago shepherl 4.3k
3
votes
4
replies
2.1k
views
What assays are distributed with Recount TX data
recount recount2 RangedSummarizedExperiment
updated 6.4 years ago by ★ 1.1k • written 7.2 years ago by ▴ 120
4
votes
5
replies
4.4k
views
How to add a color legend to plotKaryotype and kpPlotRegions ?
karyoploter
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 160
1
vote
5
replies
1.3k
views
Switching RNAseq count data to explanatory variable?
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
975
views
genbankr problem while parsing gb file
genbankr
6.4 years ago jeyp • 0
1
vote
1
reply
3.0k
views
Which one is more trustable for Cox Proportional Hazard Model with Lasso penalty? LOOCV or K-fold cross-validation?
glmnet cox LOOCV k-fold cross validation
updated 6.4 years ago by ▴ 420 • written 6.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
different designs for finding DEG by limma
limma DEG design
6.4 years ago amin.ghareyazi • 0
4
votes
5
replies
1.5k
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 6.4 years ago by • 0 • written 6.4 years ago by ▴ 20
1
vote
5
replies
2.0k
views
DESeq2: Normalization of allele specific counts in RNA-seq
deseq2 rnaseq allele-specific normalization
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
0
votes
1
reply
2.3k
views
Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
deseq2 normalization RUVg edger
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
1
reply
1.6k
views
Installation problem in IlluminaHumanMethylation450kanno.ilmn12.hg19
IlluminaHumanMethylation450kanno.ilmn12.hg19 R
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
0
votes
1
reply
7.1k
views
monocle error at orderCells
scRNA monocle packages Tutorial
6.4 years ago 444579004 • 0
2
votes
3
replies
1.7k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by ▴ 80
2
votes
2
replies
1.7k
views
DEseq2 resultsNames doesn not reproduce the right comparisons
deseq2 resultsNames()
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
vote
2
replies
2.2k
views
Rsubread package not available?
Rsubread BiocInstaller
updated 6.4 years ago by 53k • written 14.2 years ago by ▴ 410
0
votes
4
replies
2.7k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 3.1 years ago by • 0 • written 6.4 years ago by • 0
0
votes
1
reply
2.9k
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
0
votes
2
replies
1.9k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
6.4 years ago fgol ▴ 10
1
vote
1
reply
1.2k
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
1
vote
3
replies
2.2k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 6.4 years ago by ▴ 10 • written 6.4 years ago by • 0
3
votes
3
replies
1.4k
views
Is range validity checked after GRanges operations?
GenomicRanges
6.4 years ago Aditya ▴ 160
0
votes
2
replies
1.5k
views
Error while creating txDb from gtf file
genomicfeatures
6.4 years ago bioinagesh • 0
3
votes
1
reply
2.6k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
6.4 years ago ATpoint ★ 5.0k
0
votes
2
replies
1.5k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
6.5 years ago • updated 6.4 years ago Aditya ▴ 160
0
votes
2
replies
721
views
Searching for responsive genes along with a continuous variable, in environmental experimental design
edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
1
vote
4
replies
1.7k
views
gene Isoforms quantification using RNA-seq data
gene isoform quantification rna-seq
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
0
votes
2
replies
1.3k
views
GUIDEseq Error in GAlignmentPairs
GAlignmentPairs GUIDEseq
updated 6.4 years ago by ★ 4.3k • written 6.5 years ago by ▴ 10
3
votes
4
replies
1.7k
views
AnnotationDbi 1.46.0 not available in archive of Bioconductor 3.9 release?
download
updated 6.4 years ago by ▴ 160 • written 6.4 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Error using simpleaffy
software error simpleaffy genefilter
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
0
votes
0
replies
2.0k
views
Job: A post-doctoral position in bioinformatics and computational biology at Umass Medical School
single cell sequencing multi-omics data mining and integration Job
6.6 years ago • updated 6.4 years ago Julie Zhu ★ 4.3k
7
votes
4
replies
2.3k
views
seqlengths is not an exported object from namespace GenomicRanges
GenomicRanges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 160
46,743 results • Page 198 of 935
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Comment: Chip Seq Analysis of RNA Polymerase 2 by Tikaaaq2c • 0
Without proper scaling or an enrichment check , Pol 2 peaks can appear flat against the background. If the data remains noisy, you might w…
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No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
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