Showing : Alignment • reset
5
votes
12
replies
8.3k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 10.2 years ago by 52k • written 10.9 years ago by ★ 1.0k
2
votes
4
replies
7.7k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 9.8 years ago by • 0 • written 10.8 years ago by ★ 13k
0
votes
21
replies
7.6k
views
BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 16 months ago by • 0 • written 12.2 years ago by ▴ 280
0
votes
2
replies
7.0k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 11.4 years ago by ★ 11k • written 11.4 years ago by 16k
5
votes
8
replies
6.8k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
10.1 years ago ben.ward ▴ 30
0
votes
11
replies
6.4k
views
Biostring: print sequence alignment to file
Alignment Biostrings Alignment Biostrings
updated 12.9 years ago by ★ 1.7k • written 13.0 years ago by ▴ 100
1
vote
5
replies
5.2k
views
DiffBind error
Alignment DiffBind Alignment DiffBind
updated 12.2 years ago by ★ 5.2k • written 12.2 years ago by ▴ 280
0
votes
16
replies
5.0k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
6.4 years ago writetoroopali • 0
0
votes
2
replies
4.1k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.7 years ago by • 0 • written 12.0 years ago by ★ 8.2k
0
votes
1
reply
3.9k
views
how deal with multiplicate affy probes?
Alignment mgu74av2 probe affy ASSIGN Alignment mgu74av2 probe affy ASSIGN
updated 20.9 years ago by ★ 5.5k • written 20.9 years ago by ▴ 50
1
vote
1
reply
3.8k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 10
0
votes
2
replies
3.8k
views
using Blat in R
Alignment PROcess Alignment PROcess
updated 15.0 years ago by ★ 1.9k • written 15.0 years ago by ▴ 250
0
votes
6
replies
3.7k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 70
0
votes
8
replies
3.6k
views
Annotation files for bacterial genome RNAseq
Alignment Annotation ASSIGN Alignment Annotation ASSIGN
updated 10.8 years ago by 68k • written 10.8 years ago by ▴ 80
0
votes
3
replies
3.5k
views
Is there a package for peptide alignment with protein sequences?
Alignment Alignment
updated 8.6 years ago by • 0 • written 11.4 years ago by ★ 13k
0
votes
2
replies
3.3k
views
Rsamtools: sortBam() and 'samtools sort' does not give the same results
Alignment Rsamtools Alignment Rsamtools
updated 11.6 years ago by 25k • written 11.6 years ago by ★ 2.4k
0
votes
1
reply
3.3k
views
summarizeOverlaps vs countOverlaps
Alignment Alignment
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 50
0
votes
9
replies
3.3k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.3 years ago A ▴ 60
1
vote
1
reply
3.2k
views
Creat PWM from Alignment with Gaps
Alignment Cancer Alignment Cancer
updated 11.4 years ago by ▴ 250 • written 11.5 years ago by 16k
0
votes
3
replies
3.1k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome
updated 11.6 years ago by ▴ 570 • written 11.6 years ago by ▴ 40
0
votes
16
replies
3.1k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
8.5 years ago Isaac Virshup • 0
0
votes
7
replies
2.8k
views
obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
Alignment probe Alignment probe
updated 12.7 years ago by 68k • written 12.7 years ago by ★ 1.0k
1
vote
4
replies
2.8k
views
How to find the end position of a read?
rsamtools alignment cigar
7.7 years ago Frocha ▴ 20
0
votes
3
replies
2.7k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 11.8 years ago by 43k • written 11.8 years ago by ▴ 150
0
votes
2
replies
2.7k
views
alignment & SNP calling
Alignment Alignment
updated 14.4 years ago by ▴ 810 • written 14.4 years ago by ▴ 90
0
votes
3
replies
2.6k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Alignment DESeq2 Alignment DESeq2
updated 10.8 years ago by 43k • written 10.8 years ago by ▴ 30
1
vote
1
reply
2.6k
views
Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.9 years ago jcollidelcs • 0
2
votes
4
replies
2.5k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.3 years ago by • 0
0
votes
5
replies
2.5k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Biostrings Alignment Biostrings
14.7 years ago Coghlan, Avril ▴ 190
1
vote
2
replies
2.5k
views
Finding mismatches between reads and reference sequence
bsgenome cigar alignment
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 40
0
votes
1
reply
2.5k
views
Pairwise Alignment on Large Protein Sequence Data Set
Alignment genomes Alignment genomes
updated 11.3 years ago by 16k • written 11.3 years ago by ★ 13k
2
votes
1
reply
2.5k
views
Sequence Distance matrix with large sequences
Alignment Alignment
updated 11.4 years ago by 16k • written 11.4 years ago by ▴ 20
0
votes
5
replies
2.4k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ▴ 220
0
votes
9
replies
2.4k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
votes
7
replies
2.4k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment Rattus norvegicus BSgenome BSgenome QuasR Alignment Rattus norvegicus BSgenome
updated 11.1 years ago by 16k • written 11.1 years ago by ★ 4.1k
0
votes
0
replies
2.4k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
11.6 years ago Sarah Pohl ▴ 30
0
votes
7
replies
2.4k
views
about reduce function in GenomicRanges
Alignment Alignment
13.2 years ago Tarca, Adi ▴ 570
0
votes
6
replies
2.4k
views
Biostring: print sequence alignment to file
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 12.7 years ago by ▴ 100 • written 12.7 years ago by 16k
6
votes
3
replies
2.3k
views
Possible bug in Rsubread Phred-Score read
rsubread bug alignment
updated 10.4 years ago by ★ 3.6k • written 10.4 years ago by ▴ 20
0
votes
1
reply
2.3k
views
Biostrings DNAMultipleAlignment vs AlignedXStringSet
Alignment convert Alignment convert
updated 12.6 years ago by 25k • written 12.6 years ago by ★ 13k
0
votes
1
reply
2.3k
views
summarizeOverlaps vs countOverlaps
Alignment Alignment
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 50
1
vote
1
reply
2.3k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
12.0 years ago • updated 11.9 years ago Michael Stadler ▴ 350
0
votes
8
replies
2.3k
views
Rsubread alingner
Alignment Yeast Rsubread Alignment Yeast Rsubread
13.9 years ago Wei Shi ★ 3.6k
0
votes
1
reply
2.3k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 30
0
votes
1
reply
2.3k
views
It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ▴ 220
0
votes
16
replies
2.3k
views
readGAlignmentPairs error
Alignment Alignment
updated 11.5 years ago by 16k • written 11.5 years ago by ▴ 90
1
vote
2
replies
2.3k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 10
0
votes
5
replies
2.3k
views
filterBam
Alignment Alignment
updated 11.7 years ago by ▴ 500 • written 11.7 years ago by ▴ 500
0
votes
3
replies
2.2k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.3 years ago by ▴ 450 • written 4.3 years ago by • 0
0
votes
5
replies
2.2k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq quasr alignment
updated 9.3 years ago by ▴ 400 • written 9.3 years ago by • 0
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thanks James for your help! Sorry I am still a bit confused about the numerical contrast. In your example of c(0,1,0,0,0), where you are …
Answer: Merging annotation with differential expression output by James W. MacDonald 68k
This is just a general R question that you should be able to easily answer by using Google. Or you could ask on stackoverflow or biostars, …
Answer: Annotation package for Manduca sexta by shepherl 4.1k
Yes through the AnnotationHub ``` > library(AnnotationHub) > ah = AnnotationHub() snapshotDate(): 2024-10-28 > query(ah, "Manduc…
Comment: Ensembl site unresponsive via biomaRt by mdeea123 ▴ 10
Thanks for the link. I will contact them directly, I wish they had some sort of status page.
Comment: Ensembl site unresponsive via biomaRt by Mike Smith ★ 6.6k
I think this is an unrelated issue. The original post includes the message `Error: 'curl_parse_url' is not an exported object from 'namesp…
Votes
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
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