Showing : Alignment • reset
0
votes
21
replies
7.3k
views
BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 12 months ago by • 0 • written 11.9 years ago by ▴ 280
0
votes
4
replies
1.8k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
12.8 years ago delhomme@embl.de ★ 1.2k
1
vote
5
replies
5.0k
views
DiffBind error
Alignment DiffBind Alignment DiffBind
updated 11.9 years ago by ★ 5.2k • written 11.9 years ago by ▴ 280
0
votes
6
replies
3.6k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 70
0
votes
11
replies
6.1k
views
Biostring: print sequence alignment to file
Alignment Biostrings Alignment Biostrings
updated 12.7 years ago by ★ 1.7k • written 12.7 years ago by ▴ 100
0
votes
8
replies
1.8k
views
memory exhausted for readAligned
Alignment Alignment
updated 15.8 years ago by 25k • written 15.8 years ago by ★ 1.3k
2
votes
4
replies
2.4k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.0 years ago by • 0
0
votes
5
replies
1.6k
views
multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment Annotation hgu133plus2 Alignment Annotation hgu133plus2
updated 16.1 years ago by 16k • written 16.1 years ago by ▴ 10
6
votes
3
replies
2.3k
views
Possible bug in Rsubread Phred-Score read
rsubread bug alignment
updated 10.1 years ago by ★ 3.6k • written 10.1 years ago by ▴ 20
2
votes
4
replies
7.4k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 9.5 years ago by • 0 • written 10.5 years ago by ★ 13k
0
votes
5
replies
1.9k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Alignment Cancer convert GenomicAlignments Alignment Cancer convert GenomicAlignments
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 50
0
votes
5
replies
2.2k
views
filterBam
Alignment Alignment
updated 11.4 years ago by ▴ 500 • written 11.4 years ago by ▴ 500
1
vote
4
replies
2.6k
views
How to find the end position of a read?
rsamtools alignment cigar
7.5 years ago Frocha ▴ 20
0
votes
2
replies
1.2k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 40
0
votes
2
replies
1.5k
views
DEXSeq error during fold change calculation
Alignment DEXSeq Alignment DEXSeq
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ★ 13k
0
votes
3
replies
1.7k
views
Genome position to miRNA or gene name
miRNA Alignment GO Cancer BSgenome BSgenome miRNA Alignment GO Cancer BSgenome BSgenome
updated 15.9 years ago by 25k • written 15.9 years ago by ★ 1.9k
0
votes
2
replies
1.2k
views
scoring matrices
Alignment Alignment
updated 15.4 years ago by ▴ 190 • written 15.4 years ago by ▴ 870
0
votes
3
replies
1.6k
views
homopolymer gap extension penalty in Biostrings
Sequencing Alignment GO Cancer Sequencing Alignment GO Cancer
updated 12.8 years ago by ▴ 10 • written 12.8 years ago by 16k
3
votes
4
replies
1.8k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 8.4 years ago by 52k • written 8.4 years ago by • 0
0
votes
2
replies
984
views
insufficient alignment
DECIPHER Alignment
4.1 years ago julius_vn • 0
0
votes
4
replies
2.0k
views
nearly exact overlaps between GAlignmentPairs and GenomicRanges
Alignment Alignment
10.3 years ago Georg Otto ▴ 120
0
votes
8
replies
3.5k
views
Annotation files for bacterial genome RNAseq
Alignment Annotation ASSIGN Alignment Annotation ASSIGN
updated 10.5 years ago by 67k • written 10.5 years ago by ▴ 80
0
votes
3
replies
1.6k
views
edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Sequencing Alignment GO edgeR DESeq2
updated 10.3 years ago by ★ 7.9k • written 10.3 years ago by ▴ 60
0
votes
5
replies
2.1k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq quasr alignment
updated 9.0 years ago by ▴ 400 • written 9.0 years ago by • 0
0
votes
7
replies
2.2k
views
about reduce function in GenomicRanges
Alignment Alignment
12.9 years ago Tarca, Adi ▴ 570
0
votes
2
replies
3.7k
views
using Blat in R
Alignment PROcess Alignment PROcess
updated 14.7 years ago by ★ 1.9k • written 14.7 years ago by ▴ 250
0
votes
2
replies
1.6k
views
chip-seq data analysis
Transcription ChIPSeq Alignment chipseq Transcription ChIPSeq Alignment chipseq
updated 14.8 years ago by 21k • written 14.8 years ago by ▴ 60
0
votes
4
replies
1.8k
views
segfault for pairwiseAlignment
sequencing software error alignment
updated 10.2 years ago by ★ 6.5k • written 10.2 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment Cancer Biostrings IRanges Alignment Cancer Biostrings IRanges
updated 11.2 years ago by ▴ 30 • written 11.2 years ago by 16k
0
votes
16
replies
2.1k
views
readGAlignmentPairs error
Alignment Alignment
updated 11.2 years ago by 16k • written 11.3 years ago by ▴ 90
0
votes
3
replies
3.4k
views
Is there a package for peptide alignment with protein sequences?
Alignment Alignment
updated 8.3 years ago by • 0 • written 11.2 years ago by ★ 13k
0
votes
3
replies
1.6k
views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 11.6 years ago by 25k • written 11.6 years ago by ▴ 90
0
votes
8
replies
2.2k
views
Rsubread alingner
Alignment Yeast Rsubread Alignment Yeast Rsubread
13.7 years ago • updated 13.6 years ago Wei Shi ★ 3.6k
0
votes
3
replies
1.3k
views
Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 11.6 years ago by ★ 13k • written 11.6 years ago by 16k
0
votes
7
replies
2.7k
views
obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
Alignment probe Alignment probe
updated 12.4 years ago by 67k • written 12.4 years ago by ★ 1.0k
0
votes
2
replies
1.4k
views
BitSeq transcript IDs
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 11.7 years ago by ▴ 30 • written 11.7 years ago by ▴ 70
0
votes
2
replies
4.0k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.4 years ago by • 0 • written 11.7 years ago by ★ 8.2k
0
votes
6
replies
2.0k
views
Reading paired-end data into GRangesList
Alignment Alignment
updated 13.1 years ago by ▴ 970 • written 13.1 years ago by ▴ 100
0
votes
3
replies
2.0k
views
multiple feature/mode counting with summarizeOverlaps
Alignment Alignment
11.6 years ago Thomas Girke ★ 1.7k
0
votes
2
replies
6.8k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 11.1 years ago by ★ 11k • written 11.1 years ago by 16k
0
votes
2
replies
1.5k
views
EdgeR estimateTagwiseDisp()
Alignment edgeR Alignment edgeR
updated 12.0 years ago by 52k • written 12.0 years ago by ★ 13k
0
votes
5
replies
2.4k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Biostrings Alignment Biostrings
14.5 years ago • updated 14.4 years ago Coghlan, Avril ▴ 190
5
votes
12
replies
8.1k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 9.9 years ago by 52k • written 10.6 years ago by ★ 1.0k
0
votes
1
reply
882
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 15.1 years ago by 25k • written 15.1 years ago by ▴ 40
0
votes
1
reply
1.5k
views
removal of outliers in matrix
Alignment Alignment
updated 17.1 years ago by ▴ 450 • written 17.1 years ago by ▴ 20
0
votes
1
reply
1.9k
views
getSequence: difference between coding_gene_flank and 5utr
Alignment Alignment
updated 15.2 years ago by ▴ 660 • written 15.2 years ago by ▴ 220
0
votes
1
reply
3.8k
views
how deal with multiplicate affy probes?
Alignment mgu74av2 probe affy ASSIGN Alignment mgu74av2 probe affy ASSIGN
updated 20.6 years ago by ★ 5.5k • written 20.6 years ago by ▴ 50
0
votes
5
replies
1.9k
views
Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 11.8 years ago by ▴ 420 • written 11.8 years ago by ★ 11k
0
votes
1
reply
927
views
Pairwise Sequence Alignments
Alignment Alignment
updated 15.4 years ago by 21k • written 15.4 years ago by ▴ 870
0
votes
2
replies
1.1k
views
AffyProbes and genome
Microarray Alignment Annotation Cancer probe affy Microarray Alignment Annotation Cancer
updated 19.6 years ago by ▴ 20 • written 19.6 years ago by ▴ 110
50 results • Page 1 of 1
Recent ...
Replies
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag by Gordon Smyth 52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Comment: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Thanks! This one might be worth remaking with `ComplexHeatmap`. Similar to https://github.com/LieberInstitute/spatialLIBD/pull/91 that was …
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
Awards • All
Popular Question to georgii.vdovin • 0
Prophet to syednajeebashraf • 0
Popular Question to Pedro Baldoni ▴ 40
Popular Question to Wei Shi ★ 3.6k
Popular Question to Guillaume Tiberi ▴ 10
Locations • All
United Kingdom, just now
Australia, just now
Australia, 5 minutes ago
United States, 7 minutes ago
WEHI, Melbourne, Australia, 20 minutes ago
Traffic: 796 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6