Showing : Alignment • reset
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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
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16
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2.1k
views
readGAlignmentPairs error
Alignment Alignment
updated 11.2 years ago by 16k • written 11.2 years ago by ▴ 90
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16
replies
2.9k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
8.2 years ago Isaac Virshup • 0
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16
replies
4.8k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
6.1 years ago writetoroopali • 0
5
votes
12
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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
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11
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6.1k
views
Biostring: print sequence alignment to file
Alignment Biostrings Alignment Biostrings
updated 12.6 years ago by ★ 1.7k • written 12.6 years ago by ▴ 100
0
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9
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2.3k
views
visualizing alignment without realignment
msa alignment visualization
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
9
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3.0k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.0 years ago A ▴ 40
0
votes
9
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2.0k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 13.8 years ago by 21k • written 13.8 years ago by 16k
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8
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1.7k
views
memory exhausted for readAligned
Alignment Alignment
updated 15.8 years ago by 25k • written 15.8 years ago by ★ 1.3k
5
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8
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6.5k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
9.8 years ago ben.ward ▴ 30
0
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8
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3.4k
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
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8
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2.2k
views
Rsubread alingner
Alignment Yeast Rsubread Alignment Yeast Rsubread
13.6 years ago Wei Shi ★ 3.6k
0
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7
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1.8k
views
MEDIPS error extending reads
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 290
0
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7
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2.2k
views
about reduce function in GenomicRanges
Alignment Alignment
12.9 years ago Tarca, Adi ▴ 570
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7
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2.3k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment Rattus norvegicus BSgenome BSgenome QuasR Alignment Rattus norvegicus BSgenome
updated 10.8 years ago by 16k • written 10.8 years ago by ★ 4.1k
0
votes
7
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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
6
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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
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6
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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
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6
replies
2.2k
views
Biostring: print sequence alignment to file
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 12.4 years ago by ▴ 100 • written 12.4 years ago by 16k
0
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6
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1.9k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ▴ 220
0
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5
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2.2k
views
filterBam
Alignment Alignment
updated 11.4 years ago by ▴ 500 • written 11.4 years ago by ▴ 500
0
votes
5
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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
1
vote
5
replies
5.0k
views
DiffBind error
Alignment DiffBind Alignment DiffBind
updated 11.8 years ago by ★ 5.2k • written 11.9 years ago by ▴ 280
0
votes
5
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1.8k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 3.5 years ago by ▴ 150 • written 3.6 years ago by ▴ 10
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
5
replies
1.6k
views
easyRNASeq - error reading single chromosome bam
RNASeq Alignment BSgenome BSgenome RNASeq Alignment BSgenome BSgenome
updated 12.8 years ago by ★ 1.2k • written 12.8 years ago by ▴ 380
2
votes
5
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1.4k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment GO Cancer BSgenome BSgenome Alignment GO Cancer BSgenome BSgenome
updated 11.5 years ago by 25k • written 11.5 years ago by ★ 13k
0
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5
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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
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5
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1.6k
views
multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment Annotation hgu133plus2 Alignment Annotation hgu133plus2
updated 16.0 years ago by 16k • written 16.1 years ago by ▴ 10
0
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5
replies
2.3k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 10.7 years ago by ▴ 570 • written 10.7 years ago by ▴ 220
0
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5
replies
1.3k
views
GappedAlignmentPairs requests
Alignment Cancer GenomicRanges Alignment Cancer GenomicRanges
updated 12.4 years ago by ★ 11k • written 12.4 years ago by 16k
0
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5
replies
2.3k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Biostrings Alignment Biostrings
14.4 years ago Coghlan, Avril ▴ 190
0
votes
4
replies
1.7k
views
Howto annotate blast subject.id with AnnotationDbi
Alignment GO annotate AnnotationDbi Alignment GO annotate AnnotationDbi
updated 11.5 years ago by ★ 7.2k • written 11.5 years ago by ▴ 40
0
votes
4
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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
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4
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1.8k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
12.8 years ago delhomme@embl.de ★ 1.2k
2
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4
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2.4k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.0 years ago by • 0
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
2
votes
4
replies
1.6k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ★ 1.5k
0
votes
4
replies
1.6k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 7.0 years ago by 16k • written 7.0 years ago by • 0
0
votes
4
replies
1.9k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
8.7 years ago Gabriella • 0
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
4
replies
1.8k
views
WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)
Alignment Alignment
updated 11.1 years ago by ★ 11k • written 11.1 years ago by ▴ 40
0
votes
4
replies
2.0k
views
nearly exact overlaps between GAlignmentPairs and GenomicRanges
Alignment Alignment
10.3 years ago Georg Otto ▴ 120
1
vote
4
replies
2.6k
views
How to find the end position of a read?
rsamtools alignment cigar
7.4 years ago Frocha ▴ 20
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 11.3 years ago by ▴ 570 • written 11.3 years ago by ▴ 40
3
votes
3
replies
1.8k
views
Reading large DNA alignments and keeping polymorphic sites
sequence alignment biostrings
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 30
1
vote
3
replies
1.9k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 11.3 years ago by ★ 7.2k • written 11.3 years ago by ▴ 220
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
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
50 results • Page 1 of 1
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Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You can examine the structure of a `DelayedMatrix` by calling the `showtree()` function. For example: ``` library(scRNAseq) X <- fetchData…
Comment: lfcShrink and alpha value by cropero • 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states by Philippine • 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Adam • 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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