Showing : biostrings • reset
1
Vote
1
Reply
58
Views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
7 days ago Benjamin • 10 • updated 5 days ago Konstantinos Yeles • 40
2
Votes
3
Replies
80
Views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
5 weeks ago Nicholas • 0
6
Votes
5
Replies
139
Views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
7 weeks ago Bogdan • 610
1
Vote
1
Reply
73
Views
Subset center regions of a set of different length sequences
Biostrings
3 months ago ferbecneu • 0 • updated 3 months ago lahuuki • 10
0
Votes
0
Replies
58
Views
vcountPDict Out-of-Memory Errors
software error Biostrings
4 months ago jennyl.smith12 • 0
0
Votes
3
Replies
132
Views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
7 months ago skigirl618 • 0 • updated 7 months ago James W. MacDonald 56k
0
Votes
4
Replies
139
Views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
8 months ago moldach • 20
1
Vote
1
Reply
103
Views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
8 months ago anand_mt • 80 • updated 8 months ago Martin Morgan 25k
0
Votes
3
Replies
116
Views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
9 months ago Vang Le • 70 • updated 9 months ago UBodenhofer • 250
3
Votes
1
Reply
81
Views
Biostrings matchPattern with lower case
biostrings
9 months ago story.benjamin • 10 • updated 9 months ago Hervé Pagès 14k
0
Votes
0
Replies
57
Views
Detect unique deletions in DNAMultipleAlignment
biostrings
9 months ago multipleseqs • 0
0
Votes
2
Replies
79
Views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
9 months ago mb2subi • 0
1
Vote
2
Replies
64
Views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
11 months ago stephen66 • 40 • updated 11 months ago ATpoint • 390
3
Votes
1
Reply
105
Views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
12 months ago mahasish.shome • 10 • updated 12 months ago Paul Harrison • 90
2
Votes
1
Reply
98
Views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
13 months ago kalamari • 0 • updated 13 months ago Hervé Pagès 14k
1
Vote
1
Reply
119
Views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
13 months ago james.dalgleish • 30 • updated 13 months ago Martin Morgan 25k
0
Votes
1
Reply
114
Views
pairwisealignment how to normalize score?
biostrings
14 months ago marie • 0 • updated 14 months ago Hervé Pagès 14k
0
Votes
1
Reply
141
Views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
14 months ago atotalamateur • 0 • updated 14 months ago Hervé Pagès 14k
1
Vote
1
Reply
85
Views
Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
15 months ago marc.carlson • 0 • updated 15 months ago Hervé Pagès 14k
1
Vote
4
Replies
242
Views
Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
19 months ago • updated 15 months ago daniel.magnus.bader • 40
2
Votes
3
Replies
158
Views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
17 months ago Aditya • 120 • updated 16 months ago shepherl 2.5k
2
Votes
2
Replies
138
Views
vcountPDict fails on PDict
Biostrings
17 months ago Aditya • 120 • updated 17 months ago Hervé Pagès 14k
4
Votes
2
Replies
426
Views
Biostrings regex matching
Biostrings
19 months ago Aditya • 120 • updated 19 months ago Hervé Pagès 14k
0
Votes
6
Replies
197
Views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
20 months ago svetlana.gorokhova • 0 • updated 20 months ago James W. MacDonald 56k
0
Votes
0
Replies
164
Views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
21 months ago Juliet Hannah • 360
0
Votes
1
Reply
207
Views
Sensitivity and specificity in trimLRpatterns
Biostrings
22 months ago learoser • 0
5
Votes
8
Replies
694
Views
Ranges from a fasta file
biostrings fasta genomicranges granges
23 months ago Konstantinos Yeles • 40 • updated 23 months ago Martin Morgan 25k
3
Votes
3
Replies
353
Views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
24 months ago k.vitting.seerup • 100 • updated 24 months ago Michael Lawrence 11k
2
Votes
2
Replies
318
Views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
2.0 years ago aravind-j • 10 • updated 2.0 years ago Hervé Pagès 14k
0
Votes
2
Replies
820
Views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
12.0 years ago Daniel Brewer ♦ 1.9k • updated 2.0 years ago Bioconductor Community 0
1
Vote
3
Replies
291
Views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
2.1 years ago Robert Castelo ♦ 2.6k • updated 2.1 years ago Michael Lawrence 11k
0
Votes
2
Replies
350
Views
Biostrings: revComp error: Not compatible with STRSXP
biostrings Error Not compatible with STRSXP
2.1 years ago camille.4nier • 0
0
Votes
2
Replies
293
Views
Biostrings install error
biostrings install error
2.2 years ago owenchapman1 • 0
0
Votes
4
Replies
448
Views
Biostrings - translate gives wrong results for triplets TTG and CTG
biostrings
2.6 years ago janas.sebastien • 0 • updated 2.2 years ago Hervé Pagès 14k
0
Votes
0
Replies
253
Views
alphabet/encoding IlluminaQuality SolexaQuality
Biostrings XStringQuality
2.2 years ago felix.ernst • 0
1
Vote
3
Replies
339
Views
Remove reads from raw fastq
shortread biostrings
2.2 years ago ferbecneu • 0 • updated 2.2 years ago Gordon Smyth 41k
3
Votes
2
Replies
1.0k
Views
converting a fasta file to .2bit format
BioStrings rtracklayer
2.3 years ago saripalligautam86 • 10 • updated 2.3 years ago Hervé Pagès 14k
0
Votes
4
Replies
596
Views
Retrieving specific sequences from a fastq
shortread biostrings
2.3 years ago ferbecneu • 0
0
Votes
0
Replies
306
Views
Match peptide within protein sequence fasta and extract position information based on protein sequence
R seqinr biostrings
2.4 years ago rabalski • 0
0
Votes
2
Replies
479
Views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
2.4 years ago ferbecneu • 0 • updated 2.4 years ago Hervé Pagès 14k
0
Votes
1
Reply
362
Views
Cannot Update Biostrings to Latest Version
dada2 biostrings
2.5 years ago gradypierroz • 0 • updated 2.5 years ago James W. MacDonald 56k
2
Votes
2
Replies
324
Views
Biostrings: "Error in .normargSEW(start, "start")"
Biostrings
2.6 years ago Brian Smith • 120 • updated 2.6 years ago Martin Morgan 25k
0
Votes
2
Replies
307
Views
Support for BSgenomeViews objects in matchPWM
biostrings
2.7 years ago s1437643 • 10
0
Votes
1
Reply
317
Views
Biostrings translate alt_init_codons, rule doesn't apply, how to get rid of the attribution
biostrings translate
2.8 years ago XIA.PAN • 20
0
Votes
1
Reply
461
Views
Bug in Biostrings DNAStringSet(), segfault
bug biostrings
2.9 years ago ebiederstedt • 0 • updated 2.9 years ago Martin Morgan 25k
2
Votes
2
Replies
608
Views
How to combine sequences from different stringsets?
biostrings decipher
3.0 years ago reubenmcgregor88 • 0 • updated 3.0 years ago Mike Smith ♦ 4.8k
0
Votes
1
Reply
341
Views
Unexpected behavior in Biostrings::pairwiseAlignment
biostrings
3.0 years ago bc • 0 • updated 3.0 years ago Hervé Pagès 14k
0
Votes
3
Replies
455
Views
How to find multiple overlaps with pairwiseAlignment()?
biostrings pairwisealignment
3.0 years ago kgorczak • 10 • updated 3.0 years ago Hervé Pagès 14k
2
Votes
1
Reply
379
Views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
3.0 years ago xieduo • 10 • updated 3.0 years ago shepherl 2.5k
0
Votes
2
Replies
543
Views
Error in pairwiseAlignment when considering an empty seuqnece
biostrings
4.6 years ago kristoffer.vittingseerup • 20 • updated 3.0 years ago Hervé Pagès