Showing : Biostrings • reset
0
votes
0
replies
1.1k
views
vcountPDict Out-of-Memory Errors
software error Biostrings
5.3 years ago JennyS • 0
0
votes
3
replies
2.4k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
4
replies
3.5k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
5.7 years ago moldach ▴ 20
1
vote
1
reply
1.2k
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 90
0
votes
3
replies
2.0k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 5.8 years ago by ▴ 300 • written 5.8 years ago by ▴ 80
3
votes
1
reply
1.4k
views
Biostrings matchPattern with lower case
biostrings
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 20
0
votes
0
replies
856
views
Detect unique deletions in DNAMultipleAlignment
biostrings
5.8 years ago multipleseqs • 0
0
votes
2
replies
1.5k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
5.8 years ago mb2subi • 0
1
vote
2
replies
1.3k
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 6.0 years ago by ★ 5.0k • written 6.0 years ago by ▴ 50
5
votes
1
reply
4.6k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 6.0 years ago by ▴ 110 • written 6.0 years ago by ▴ 20
2
votes
1
reply
1.0k
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 6.1 years ago by 16k • written 6.1 years ago by • 0
1
vote
1
reply
1.3k
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 30
0
votes
1
reply
1.1k
views
pairwisealignment how to normalize score?
biostrings
updated 6.2 years ago by 16k • written 6.2 years ago by • 0
0
votes
1
reply
1.6k
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 6.2 years ago by 16k • written 6.2 years ago by • 0
1
vote
1
reply
973
views
Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
updated 6.2 years ago by 16k • written 6.2 years ago by • 0
1
vote
4
replies
2.5k
views
Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
6.6 years ago • updated 6.3 years ago daniel.magnus.bader ▴ 50
2
votes
3
replies
2.0k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 6.4 years ago by 4.3k • written 6.4 years ago by ▴ 160
2
votes
2
replies
1.3k
views
vcountPDict fails on PDict
Biostrings
updated 6.4 years ago by 16k • written 6.5 years ago by ▴ 160
4
votes
2
replies
2.8k
views
Biostrings regex matching
Biostrings
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 160
0
votes
6
replies
1.7k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
votes
0
replies
1.1k
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
6.7 years ago Juliet Hannah ▴ 360
0
votes
1
reply
952
views
Sensitivity and specificity in trimLRpatterns
Biostrings
6.9 years ago learoser • 0
6
votes
8
replies
4.0k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 90
3
votes
3
replies
2.0k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 120
2
votes
2
replies
1.4k
views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 20
0
votes
2
replies
2.2k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 7.0 years ago by 0 • written 17.0 years ago by ★ 1.9k
1
vote
3
replies
1.7k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ★ 3.4k
0
votes
2
replies
2.0k
views
Biostrings: revComp error: Not compatible with STRSXP
biostrings Error Not compatible with STRSXP
7.1 years ago camille.4nier • 0
0
votes
2
replies
1.6k
views
Biostrings install error
biostrings install error
7.2 years ago owenchapman1 • 0
0
votes
4
replies
2.0k
views
Biostrings - translate gives wrong results for triplets TTG and CTG
biostrings
updated 7.2 years ago by 16k • written 7.6 years ago by • 0
0
votes
0
replies
894
views
alphabet/encoding IlluminaQuality SolexaQuality
Biostrings XStringQuality
7.2 years ago felix.ernst • 0
1
vote
3
replies
2.2k
views
Remove reads from raw fastq
shortread biostrings
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
3
votes
2
replies
5.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 10
0
votes
4
replies
5.7k
views
Retrieving specific sequences from a fastq
shortread biostrings
7.3 years ago ferbecneu • 0
0
votes
0
replies
1.6k
views
Match peptide within protein sequence fasta and extract position information based on protein sequence
R seqinr biostrings
7.4 years ago rabalski • 0
0
votes
2
replies
1.8k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 7.4 years ago by 16k • written 7.4 years ago by • 0
0
votes
1
reply
1.5k
views
Cannot Update Biostrings to Latest Version
dada2 biostrings
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
2
votes
2
replies
1.2k
views
Biostrings: "Error in .normargSEW(start, "start")"
Biostrings
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 120
0
votes
2
replies
1.0k
views
Support for BSgenomeViews objects in matchPWM
biostrings
7.7 years ago s1437643 ▴ 20
0
votes
1
reply
1.1k
views
Biostrings translate alt_init_codons, rule doesn't apply, how to get rid of the attribution
biostrings translate
7.8 years ago XIA.PAN ▴ 20
1
vote
1
reply
1.5k
views
Bug in Biostrings DNAStringSet(), segfault
bug biostrings
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 10
2
votes
2
replies
2.9k
views
How to combine sequences from different stringsets?
biostrings decipher
updated 8.0 years ago by ★ 6.6k • written 8.0 years ago by • 0
0
votes
1
reply
897
views
Unexpected behavior in Biostrings::pairwiseAlignment
biostrings
updated 8.0 years ago by 16k • written 8.0 years ago by • 0
0
votes
3
replies
2.1k
views
How to find multiple overlaps with pairwiseAlignment()?
biostrings pairwisealignment
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 10
2
votes
1
reply
1.4k
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 8.0 years ago by 4.3k • written 8.0 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Error in pairwiseAlignment when considering an empty seuqnece
biostrings
updated 8.0 years ago by 16k • written 9.6 years ago by ▴ 20
5
votes
7
replies
2.5k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 8.0 years ago by ▴ 150 • written 8.0 years ago by • 0
0
votes
2
replies
1.5k
views
Is it possible to import many .tsr sequence file into R using bio strings for use in DECIPHER?
r biostrings decipher
8.1 years ago reubenmcgregor88 • 0
2
votes
5
replies
2.5k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by • 0
2
votes
3
replies
2.6k
views
Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher DNA biostrings
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by • 0
292 results • Page 2 of 6
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
Poland, 6 minutes ago
United States, 32 minutes ago
Canada, 39 minutes ago
United States, 1 hour ago
Germany, 1 hour ago
Traffic: 1537 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6