Showing : BioStrings • reset
8
votes
3
replies
3.3k
views
Algorithm description for matchPWM (Biostrings)
biostrings matchPWM
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 370
6
votes
5
replies
1.5k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago Bogdan ▴ 670
6
votes
8
replies
2.7k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 80
6
votes
11
replies
2.9k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 9.4 years ago by ▴ 180 • written 9.4 years ago by ▴ 40
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
6
votes
6
replies
2.5k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges biostrings bsapply BSgenome
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 70
5
votes
20
replies
3.1k
views
matching of AAStringSet vs. another AAStringSet
biostrings AAStringset
7.4 years ago tobias.kockmann ▴ 20
5
votes
1
reply
1.7k
views
Chromosome position to nucleotide - Biostrings?
biostrings
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 120
5
votes
8
replies
6.0k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
9.2 years ago ben.ward ▴ 30
5
votes
7
replies
1.6k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 6.3 years ago by ▴ 150 • written 6.3 years ago by • 0
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 70
5
votes
1
reply
3.1k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 4.3 years ago by ▴ 100 • written 4.3 years ago by ▴ 20
5
votes
5
replies
1.4k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago Sam • 0
5
votes
15
replies
3.1k
views
problem with QDNAseq's createBins for new BSgenome package
bsgenome biostrings qdnaseq pfalciparum
updated 8.7 years ago by ▴ 50 • written 8.7 years ago by • 0
4
votes
7
replies
1.5k
views
how to catch an error when using subseq() in vectorized way
biostrings subseq
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 20
4
votes
2
replies
1.9k
views
Biostrings regex matching
Biostrings
updated 4.9 years ago by 16k • written 4.9 years ago by ▴ 160
4
votes
7
replies
1.4k
views
Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
Biostrings
7.8 years ago • updated 7.7 years ago matt.chambers42 ▴ 10
4
votes
5
replies
1.2k
views
XStringSet operations discard names - how to address?
biostrings
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
4
votes
1
reply
993
views
IRanges, Partitioning by End function not found.
IRanges Biostrings
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 30
4
votes
9
replies
1.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 250
4
votes
5
replies
2.6k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings pairwiseAlignment
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 120
4
votes
13
replies
4.4k
views
How to create an output file with sequence ID's from multiple BLAST result using blastSequences in "Biostrings"
annotation blast biostrings
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
3
votes
2
replies
1.4k
views
pairwiseAlignments coordinate mapping?
biostrings pairwisealignment
updated 7.9 years ago by 16k • written 7.9 years ago by ★ 13k
3
votes
2
replies
4.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 5.5 years ago by 16k • written 5.5 years ago by ▴ 10
3
votes
3
replies
1.3k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 120
3
votes
2
replies
1.3k
views
Get a complete view of a long DNA sequence of a Biostrings object in R
biostrings subsetting View dnastring dnaseq
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
3
votes
5
replies
1.4k
views
Biostrings multiple pattern match
pattern Biostrings
updated 18 months ago by 16k • written 18 months ago by • 0
3
votes
2
replies
1.7k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago • updated 3.2 years ago Benjamin ▴ 20
3
votes
3
replies
1.6k
views
Reading large DNA alignments and keeping polymorphic sites
sequence alignment biostrings
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 30
3
votes
4
replies
1.4k
views
findComplementedPalindromes function is not finding all complementary palindromes
Biostrings
updated 9.4 years ago by 16k • written 9.4 years ago by • 0
3
votes
1
reply
945
views
Biostrings matchPattern with lower case
biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 20
2
votes
4
replies
1.2k
views
Ranges on AAStrings
AAString Views Biostrings
7.2 years ago tobias.kockmann ▴ 20
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ★ 1.5k
2
votes
2
replies
1.1k
views
Creating a Biostrings PDict object from amino-acid sequences
biostrings pdict
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 110
2
votes
4
replies
4.2k
views
What is the best way to subset a DNAStringSet by a GRange ?
bioconductor biostrings granges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by • 0
2
votes
2
replies
979
views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 20
2
votes
1
reply
1.0k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 7.9 years ago by 16k • written 7.9 years ago by ▴ 40
2
votes
2
replies
886
views
vcountPDict fails on PDict
Biostrings
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 160
2
votes
2
replies
919
views
Trim a variable number of bases off read, depending on read length
Biostrings
8.1 years ago knaxerova ▴ 10
2
votes
2
replies
1.1k
views
Exclude masked rownames in DNAMultipleAlignments
multiple sequences masks rowmask rownames biostrings
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 30
2
votes
5
replies
1.6k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 6.3 years ago by ▴ 150 • written 6.3 years ago by • 0
2
votes
1
reply
937
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 6.3 years ago by 3.8k • written 6.3 years ago by ▴ 10
2
votes
3
replies
1.2k
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment biostrings
8.6 years ago vincent.plagnol ▴ 10
2
votes
4
replies
1.3k
views
vcountPattern for Pattern Contained within or Containing Subject
biostrings countpattern
8.5 years ago Dario Strbenac ★ 1.5k
2
votes
2
replies
2.2k
views
msa: How to obtain a subset of an alignment
msa Biostrings MultipleAlignment
updated 6.6 years ago by ▴ 290 • written 6.6 years ago by ▴ 10
2
votes
1
reply
1.0k
views
Error in score() function on pairwiseAlignment()
biostrings pairwisealignment
updated 8.0 years ago by 3.8k • written 8.0 years ago by • 0
2
votes
3
replies
1.8k
views
Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher DNA biostrings
updated 6.3 years ago by ▴ 150 • written 6.3 years ago by • 0
2
votes
2
replies
1.9k
views
How to combine sequences from different stringsets?
biostrings decipher
updated 6.2 years ago by ★ 6.5k • written 6.2 years ago by • 0
2
votes
2
replies
1.4k
views
"Wobble" patterns for genome searching using Biostrings
biostrings bsgenome motif RGYW
8.8 years ago fongchunchan ▴ 30
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Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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