Showing : bsgenome • reset
0
votes
5
replies
2.0k
views
matchPattern vmatchPattern vectorised
BSgenome BSgenome BSgenome BSgenome
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ★ 13k
0
votes
0
replies
2.3k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
11.8 years ago Hervé Pagès 16k
0
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0
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2.4k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
11.8 years ago Hervé Pagès 16k
0
votes
0
replies
852
views
BSgenome.Mmulatta.UCSC
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
11.9 years ago Hervé Pagès 16k
0
votes
2
replies
1.9k
views
Question about ReportingTools used with DESeq2
GO BSgenome BSgenome ReportingTools DESeq2 GO BSgenome BSgenome ReportingTools DESeq2
updated 11.9 years ago by 68k • written 11.9 years ago by ▴ 80
0
votes
7
replies
3.4k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 11.9 years ago by ★ 1.2k • written 11.9 years ago by ★ 13k
0
votes
0
replies
932
views
A question for QuasR::qQCReport
BSgenome BSgenome BSgenome BSgenome
11.9 years ago Michael Stadler ▴ 350
0
votes
2
replies
2.3k
views
BSgenome.Mmusculus.UCSC.mm10 and upstream sequences.
Mus musculus BSgenome BSgenome Mus musculus BSgenome BSgenome
updated 11.9 years ago by 16k • written 11.9 years ago by ▴ 760
0
votes
0
replies
2.2k
views
Create a sample file /tab delimited file in QuasR
BSgenome convert BSgenome genomes QuasR BSgenome convert BSgenome genomes QuasR
12.0 years ago Michael Stadler ▴ 350
0
votes
0
replies
1.7k
views
Create a sample file /tab delimited file in QuasR
BSgenome convert BSgenome QuasR BSgenome convert BSgenome QuasR
12.0 years ago Guest User ★ 13k
0
votes
3
replies
3.8k
views
Working with ensembl 73 & BSGenome
Annotation BSgenome TranscriptDb biomaRt BSgenome Annotation BSgenome TranscriptDb biomaRt
updated 12.0 years ago by 16k • written 12.0 years ago by ★ 13k
0
votes
0
replies
2.0k
views
working with genome-wide phastCons scores
BSgenome convert BSgenome rtracklayer IRanges charm BSgenome convert BSgenome rtracklayer
12.0 years ago Robert Castelo ★ 3.4k
0
votes
1
reply
1.0k
views
BStringSet not work with lists of many DNAString elements
BSgenome convert BSgenome BSgenome convert BSgenome
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 360
0
votes
7
replies
3.2k
views
QuasR on Linux Cluster
BSgenome BSgenome QuasR BSgenome BSgenome QuasR
updated 12.0 years ago by ▴ 350 • written 12.0 years ago by ▴ 340
0
votes
13
replies
2.1k
views
Retreving mRNA subsequence (GenomicFeatures, BSgenome)
BSgenome BSgenome BSgenome BSgenome
updated 12.0 years ago by ▴ 210 • written 12.0 years ago by ★ 13k
0
votes
0
replies
939
views
help with forging a BSgenome data
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.0 years ago Hervé Pagès 16k
0
votes
1
reply
3.9k
views
org.Hs.eg.db
BSgenome BSgenome BSgenome BSgenome
updated 12.0 years ago by 68k • written 12.0 years ago by ★ 13k
0
votes
5
replies
3.5k
views
Biostrings::matchPattern,extract sequences
GO BSgenome BSgenome GO BSgenome BSgenome
updated 12.1 years ago by 16k • written 12.1 years ago by ★ 4.3k
0
votes
1
reply
1.2k
views
MEDIPS saturation error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.1 years ago by ▴ 40 • written 12.1 years ago by ★ 13k
0
votes
1
reply
882
views
alignShortReads
BSgenome BSgenome BSgenome BSgenome
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 10
0
votes
3
replies
3.3k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome
updated 12.2 years ago by ▴ 570 • written 12.2 years ago by ▴ 40
0
votes
4
replies
1.5k
views
I need BSgenome for Eucalyptus grandis
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
updated 12.2 years ago by ★ 7.2k • written 12.2 years ago by ★ 13k
0
votes
5
replies
2.2k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.2 years ago Alan Smith ▴ 150
0
votes
0
replies
1.4k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.2 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.5k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.2 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.3k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts
Annotation GO BSgenome BSgenome Annotation GO BSgenome BSgenome
12.2 years ago Alan Smith ▴ 150
0
votes
3
replies
1.9k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
12.2 years ago Alan Smith ▴ 150
0
votes
0
replies
1.9k
views
Bsgenome gap mask conundrum
BSgenome BSgenome BSgenome BSgenome
12.2 years ago Ugo Borello ▴ 340
0
votes
2
replies
1.8k
views
Blast a BSgenome
BSgenome BSgenome BSgenome BSgenome
updated 12.3 years ago by 16k • written 12.3 years ago by ▴ 340
0
votes
1
reply
1.8k
views
problem with 'FDb.InfiniumMethylation.hg19'
BSgenome BSgenome lumi methylumi BSgenome BSgenome lumi methylumi
updated 12.3 years ago by ▴ 120 • written 12.3 years ago by 68k
0
votes
2
replies
1.7k
views
lumiR returns ExpressionSet object instead of LumiBatch
GO Mus musculus BSgenome BSgenome lumi GO Mus musculus BSgenome BSgenome lumi
updated 12.3 years ago by ▴ 440 • written 12.3 years ago by ★ 13k
2
votes
4
replies
8.1k
views
merging GRange objects
Annotation BSgenome BSgenome Annotation BSgenome BSgenome
updated 12.3 years ago by 16k • written 12.3 years ago by ★ 13k
0
votes
5
replies
1.9k
views
TXNAME mapping
GO BSgenome BSgenome GO BSgenome BSgenome
updated 12.3 years ago by ▴ 90 • written 12.3 years ago by ★ 13k
0
votes
3
replies
1.1k
views
comparing seqnames
BSgenome BSgenome BSgenome BSgenome
updated 12.3 years ago by 25k • written 12.3 years ago by ★ 13k
2
votes
5
replies
1.7k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment GO Cancer BSgenome BSgenome Alignment GO Cancer BSgenome BSgenome
updated 12.3 years ago by 25k • written 12.3 years ago by ★ 13k
1
vote
1
reply
1.6k
views
import gene annotations from genbank
BSgenome BSgenome BSgenome BSgenome
updated 12.4 years ago by ▴ 400 • written 12.4 years ago by ★ 13k
0
votes
2
replies
1.7k
views
ChIPpeakAnno makeVennDiagram problems
GO BSgenome BSgenome ChIPpeakAnno GO BSgenome BSgenome ChIPpeakAnno
updated 12.4 years ago by ★ 4.3k • written 12.4 years ago by ▴ 160
0
votes
8
replies
4.0k
views
QuasR: how to use an indexed reference genome?
BSgenome BSgenome genomes QuasR BSgenome BSgenome genomes QuasR
updated 12.4 years ago by ▴ 350 • written 12.4 years ago by ▴ 750
0
votes
1
reply
1.5k
views
gmapR problem using a GmapGenome package with gsnap()
GO BSgenome BSgenome gmapR GO BSgenome BSgenome gmapR
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ★ 3.4k
0
votes
3
replies
1.4k
views
Migrating a Large BSgenome Package to R 3.0
BSgenome BSgenome BSgenome BSgenome
updated 12.4 years ago by 16k • written 12.5 years ago by ★ 1.6k
0
votes
0
replies
1.4k
views
REDseq_question
Sequencing Genetics BSgenome BSgenome REDseq Sequencing Genetics BSgenome BSgenome REDseq
12.5 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.4k
views
it is strange that I cannot get the fpkm by using easyRNASeq
Annotation BSgenome BSgenome easyRNASeq Annotation BSgenome BSgenome easyRNASeq
updated 12.5 years ago by ▴ 30 • written 12.5 years ago by ★ 13k
0
votes
7
replies
2.1k
views
MEDIPS error extending reads
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 12.5 years ago by ▴ 570 • written 12.5 years ago by ▴ 290
0
votes
1
reply
780
views
Error: package ŒGenomicRanges¹ 1.11.45 was found, but >= 1.11.46 is required by ŒBSgenome¹
BSgenome BSgenome BSgenome BSgenome
12.5 years ago Ou, Jianhong ★ 1.3k
0
votes
5
replies
5.7k
views
Finding mismatches between reads and reference sequence
Infrastructure Cancer BSgenome BSgenome Infrastructure Cancer BSgenome BSgenome
updated 12.5 years ago by ▴ 30 • written 12.5 years ago by 16k
0
votes
3
replies
2.3k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 12.5 years ago by 68k • written 12.5 years ago by ★ 2.0k
0
votes
2
replies
1.8k
views
Limit on number of sequence files for forging a BSgenome
GO Cancer BSgenome BSgenome genomes GO Cancer BSgenome BSgenome genomes
12.5 years ago Hervé Pagès 16k
0
votes
0
replies
1.9k
views
Bioconductor Digest, Vol 121, Issue 29
miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn
12.5 years ago Matthew Thornton ▴ 380
0
votes
0
replies
1.0k
views
Problems in running easyRNASeq
Annotation BSgenome BSgenome Annotation BSgenome BSgenome
12.5 years ago pepap ▴ 10
3
votes
4
replies
1.6k
views
Limit on number of sequence files for forging a BSgenome
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 12.6 years ago by ★ 6.5k • written 12.6 years ago by ▴ 220
349 results • Page 4 of 7
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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