Showing : Biostrings • reset
1
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9
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3.5k
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Handling DNA sequence loaded from a file
r biostrings DNAsequence
updated 3.4 years ago by 68k • written 9.6 years ago by ▴ 260
0
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2
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1.6k
views
Error: no slot of name "start" for this object of class "XStringViews"
XStringViews biostrings
9.7 years ago • updated 9.6 years ago jbtouching • 0
0
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0
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950
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Pointer to unstrsplit from XStringSetList-class man page
biostrings DNAStringSetList
9.6 years ago Michael Love 43k
0
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0
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1.9k
views
Error in Biostrings::pairwiseAlignment() 'vals' must be a vector of the length of 'keys'
biostrings
9.6 years ago Daniel Cameron ▴ 40
2
votes
2
replies
1.3k
views
Trim a variable number of bases off read, depending on read length
Biostrings
9.6 years ago knaxerova ▴ 10
0
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5
replies
3.8k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
9.6 years ago • updated 17 months ago Henrik Bengtsson ★ 2.4k
1
vote
3
replies
1.8k
views
calculate frequency of non-overlapping matches for a motif in a XStringSet
Biostrings patternmatch biostrings matchpattern
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 40
4
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1
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1.3k
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IRanges, Partitioning by End function not found.
IRanges Biostrings
updated 9.8 years ago by 25k • written 9.8 years ago by ▴ 30
0
votes
1
reply
1.8k
views
vmatchpattern with indexed fasta files
fasta fai vmatchpattern biostrings
updated 9.8 years ago by 16k • written 10.0 years ago by • 0
2
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2
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1.4k
views
Exclude masked rownames in DNAMultipleAlignments
multiple sequences masks rowmask rownames biostrings
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by ▴ 30
0
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3
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2.4k
views
The way to window over sequences of a DNAStringSet
biostrings window mask views
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 30
1
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1
reply
1.1k
views
Error with DNAStringSet
biostrings iranges
updated 9.9 years ago by 25k • written 9.9 years ago by • 0
4
votes
7
replies
2.8k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 20
1
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1
reply
2.8k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 10
2
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4
replies
1.7k
views
vcountPattern for Pattern Contained within or Containing Subject
biostrings countpattern
10.0 years ago Dario Strbenac ★ 1.6k
0
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1
reply
1.6k
views
pairwiseAlignment() - Similarity NA% ?
biostrings pairwisealignment
updated 10.0 years ago by 16k • written 10.0 years ago by • 0
2
votes
3
replies
1.5k
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment biostrings
10.1 years ago vincent.plagnol ▴ 10
1
vote
1
reply
1.4k
views
Forge a BSgenome data package
bsgenome biostrings Gviz
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 40
0
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2
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2.1k
views
inconsistent pairwiseAlignment behaviour (Biostrings) with multiple alignments with identical scores
biostrings pairwisealignment
10.1 years ago vincent.plagnol ▴ 10
0
votes
1
reply
1.8k
views
Biostrings: problem to access indel-details (nucleotide sequence) form pairwiseAlignment()
bioconductor biostrings
updated 10.1 years ago by 16k • written 10.1 years ago by • 0
3
votes
2
replies
1.8k
views
Get a complete view of a long DNA sequence of a Biostrings object in R
biostrings subsetting View dnastring dnaseq
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
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1
reply
2.4k
views
Map siRNA-Sequence to Gene
sequence annotationhub biostrings
updated 10.2 years ago by 16k • written 10.2 years ago by • 0
1
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7
replies
3.0k
views
Biostrings pairwiseAligment() output shorter than source sequence
Biostrings
10.2 years ago jean.peccoud • 0
5
votes
15
replies
4.2k
views
problem with QDNAseq's createBins for new BSgenome package
bsgenome biostrings qdnaseq pfalciparum
updated 10.2 years ago by ▴ 50 • written 10.2 years ago by • 0
0
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4
replies
4.0k
views
Biostrings throwing error
biostrings installation package keepNA
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
votes
1
reply
2.0k
views
Counting SNPs where ambiguity codes represent heterozygosity.
Biostrings SNPs alignment
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 30
4
votes
13
replies
5.9k
views
How to create an output file with sequence ID's from multiple BLAST result using blastSequences in "Biostrings"
annotation blast biostrings
updated 10.3 years ago by 25k • written 10.3 years ago by • 0
2
votes
2
replies
1.9k
views
"Wobble" patterns for genome searching using Biostrings
biostrings bsgenome motif RGYW
10.3 years ago fongchunchan ▴ 30
0
votes
1
reply
1.1k
views
Identical() fails in Biostrings package
biostrings bug
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 20
1
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1
reply
1.1k
views
writePairwiseAlignments returns error
biostrings
updated 10.4 years ago by 16k • written 10.4 years ago by • 0
5
votes
8
replies
7.2k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
10.7 years ago ben.ward ▴ 30
3
votes
3
replies
2.1k
views
Reading large DNA alignments and keeping polymorphic sites
sequence alignment biostrings
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 30
2
votes
1
reply
1.5k
views
Comparing AAStrings using identical() instead of ==
AAstring Biostrings == identical
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 10
3
votes
4
replies
1.8k
views
findComplementedPalindromes function is not finding all complementary palindromes
Biostrings
updated 10.9 years ago by 16k • written 10.9 years ago by • 0
2
votes
2
replies
2.3k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
11.0 years ago b.stielow • 0
6
votes
11
replies
4.3k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 11.0 years ago by ▴ 180 • written 11.0 years ago by ▴ 40
4
votes
5
replies
3.4k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings pairwiseAlignment
updated 11.0 years ago by 16k • written 11.0 years ago by ▴ 120
5
votes
1
reply
2.2k
views
Chromosome position to nucleotide - Biostrings?
biostrings
updated 11.0 years ago by ★ 1.3k • written 11.0 years ago by ▴ 120
2
votes
1
reply
2.7k
views
getSeq with GRanges object error: function not found
biostrings bsgenome granges
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 20
8
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3
replies
3.9k
views
Algorithm description for matchPWM (Biostrings)
biostrings matchPWM
updated 11.1 years ago by 16k • written 11.1 years ago by ▴ 370
0
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0
replies
1.2k
views
[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method
GO Biostrings rtracklayer GenomicRanges BiocParallel GenomicFiles
11.1 years ago Dan Tenenbaum ★ 8.2k
0
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1
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1.3k
views
Putative bug in Biostrings
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 11.3 years ago by ▴ 10 • written 11.3 years ago by 16k
0
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1
reply
2.0k
views
Biostrings readDNAMultipleAlignment broken for fasta input
Alignment Biostrings Alignment Biostrings
updated 11.3 years ago by 16k • written 11.3 years ago by ▴ 740
0
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3
replies
2.2k
views
Creating a package
Saccharomyces cerevisiae BSgenome Biostrings BSgenome Saccharomyces cerevisiae BSgenome
updated 11.4 years ago by 68k • written 11.4 years ago by ★ 13k
0
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3
replies
2.0k
views
Elephant shark genome
Biostrings genomes Biostrings genomes
updated 11.5 years ago by 25k • written 11.5 years ago by ★ 13k
0
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0
replies
1.7k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
11.6 years ago Guest User ★ 13k
0
votes
9
replies
2.6k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.7 years ago by 16k • written 11.7 years ago by ▴ 740
0
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1
reply
1.3k
views
substr on XStringSet-class
Biostrings Biostrings
updated 11.8 years ago by 16k • written 11.9 years ago by ★ 13k
0
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0
replies
1.9k
views
Easy way to convert CharacterList to character, collapsing each element?
Annotation Cancer Biostrings IRanges Annotation Cancer Biostrings IRanges
11.9 years ago Hervé Pagès 16k
0
votes
1
reply
5.7k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 11.9 years ago by ▴ 280 • written 11.9 years ago by 16k
292 results • Page 4 of 6
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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