Showing : Biostrings • reset
4
votes
9
replies
208
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 8 days ago by 15k • written 21 days ago by ▴ 180
0
votes
0
replies
80
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
11 weeks ago adklts • 0
0
votes
3
replies
150
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
12 weeks ago • updated 10 weeks ago sieminsk • 0
3
votes
2
replies
181
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
5 months ago • updated 4 months ago Benjamin ▴ 20
2
votes
3
replies
160
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
6 months ago Nicholas • 0
6
votes
5
replies
243
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
6 months ago Bogdan ▴ 610
1
vote
1
reply
125
views
Subset center regions of a set of different length sequences
Biostrings
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
0
votes
0
replies
101
views
vcountPDict Out-of-Memory Errors
software error Biostrings
8 months ago jennyl.smith12 • 0
0
votes
3
replies
219
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 12 months ago by 57k • written 12 months ago by • 0
0
votes
4
replies
328
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
12 months ago moldach ▴ 20
1
vote
1
reply
155
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 13 months ago by 25k • written 13 months ago by ▴ 80
0
votes
3
replies
202
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 14 months ago by ▴ 260 • written 14 months ago by ▴ 70
3
votes
1
reply
149
views
Biostrings matchPattern with lower case
biostrings
updated 14 months ago by 15k • written 14 months ago by ▴ 10
0
votes
0
replies
100
views
Detect unique deletions in DNAMultipleAlignment
biostrings
14 months ago multipleseqs • 0
0
votes
2
replies
165
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
14 months ago mb2subi • 0
1
vote
2
replies
123
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 16 months ago by ▴ 640 • written 16 months ago by ▴ 50
3
votes
1
reply
228
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 17 months ago by ▴ 90 • written 17 months ago by ▴ 10
2
votes
1
reply
148
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 18 months ago by 15k • written 18 months ago by • 0
1
vote
1
reply
180
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 18 months ago by 25k • written 18 months ago by ▴ 30
0
votes
1
reply
178
views
pairwisealignment how to normalize score?
biostrings
updated 19 months ago by 15k • written 19 months ago by • 0
0
votes
1
reply
232
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 19 months ago by 15k • written 19 months ago by • 0
1
vote
1
reply
139
views
Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
updated 20 months ago by 15k • written 20 months ago by • 0
1
vote
4
replies
376
views
Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
2.0 years ago • updated 20 months ago daniel.magnus.bader ▴ 40
2
votes
3
replies
219
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 21 months ago by 2.7k • written 22 months ago by ▴ 120
2
votes
2
replies
198
views
vcountPDict fails on PDict
Biostrings
updated 22 months ago by 15k • written 22 months ago by ▴ 120
4
votes
2
replies
578
views
Biostrings regex matching
Biostrings
updated 2.0 years ago by 15k • written 2.0 years ago by ▴ 120
0
votes
6
replies
292
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 2.1 years ago by 57k • written 2.1 years ago by • 0
0
votes
0
replies
214
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
2.1 years ago Juliet Hannah ▴ 360
0
votes
1
reply
263
views
Sensitivity and specificity in trimLRpatterns
Biostrings
2.3 years ago learoser • 0
5
votes
8
replies
901
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 2.3 years ago by 25k • written 2.3 years ago by ▴ 60
3
votes
3
replies
444
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 100
2
votes
2
replies
390
views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
updated 2.4 years ago by 15k • written 2.4 years ago by ▴ 20
0
votes
2
replies
882
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 2.4 years ago by 0 • written 12.4 years ago by ★ 1.9k
1
vote
3
replies
355
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 2.5 years ago by 11k • written 2.5 years ago by ★ 2.7k
0
votes
2
replies
437
views
Biostrings: revComp error: Not compatible with STRSXP
biostrings Error Not compatible with STRSXP
2.5 years ago camille.4nier • 0
0
votes
2
replies
364
views
Biostrings install error
biostrings install error
2.6 years ago owenchapman1 • 0
0
votes
4
replies
525
views
Biostrings - translate gives wrong results for triplets TTG and CTG
biostrings
updated 2.6 years ago by 15k • written 3.0 years ago by • 0
0
votes
0
replies
297
views
alphabet/encoding IlluminaQuality SolexaQuality
Biostrings XStringQuality
2.6 years ago felix.ernst • 0
1
vote
3
replies
414
views
Remove reads from raw fastq
shortread biostrings
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
3
votes
2
replies
1.2k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 2.7 years ago by 15k • written 2.7 years ago by ▴ 10
0
votes
4
replies
795
views
Retrieving specific sequences from a fastq
shortread biostrings
2.7 years ago ferbecneu • 0
0
votes
0
replies
379
views
Match peptide within protein sequence fasta and extract position information based on protein sequence
R seqinr biostrings
2.8 years ago rabalski • 0
0
votes
2
replies
585
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 2.8 years ago by 15k • written 2.8 years ago by • 0
0
votes
1
reply
416
views
Cannot Update Biostrings to Latest Version
dada2 biostrings
updated 2.9 years ago by 57k • written 2.9 years ago by • 0
2
votes
2
replies
381
views
Biostrings: "Error in .normargSEW(start, "start")"
Biostrings
updated 3.0 years ago by 25k • written 3.0 years ago by ▴ 120
0
votes
2
replies
367
views
Support for BSgenomeViews objects in matchPWM
biostrings
3.1 years ago s1437643 ▴ 10
0
votes
1
reply
361
views
Biostrings translate alt_init_codons, rule doesn't apply, how to get rid of the attribution
biostrings translate
3.2 years ago XIA.PAN ▴ 20
0
votes
1
reply
521
views
Bug in Biostrings DNAStringSet(), segfault
bug biostrings
updated 3.3 years ago by 25k • written 3.3 years ago by • 0
2
votes
2
replies
707
views
How to combine sequences from different stringsets?
biostrings decipher
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
votes
1
reply
380
views
Unexpected behavior in Biostrings::pairwiseAlignment
biostrings
updated 3.4 years ago by 15k • written 3.4 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Data input for aracne2regulon function in viper package by Keith Hughitt ▴ 130
Hi, I'm afraid not, so I don't think I can be much help, unfortunately. In the past, the authors of ARACNe-AP were generally quite responsi…
Comment: Data input for aracne2regulon function in viper package by Luna_P • 0
Hello Keith, I am currently trying to use my ARACNE-AP generated networks in Viper. I did all three steps you mentioned above but my prob…
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
Awards • All
Popular Question to Keith Hughitt ▴ 130
Scholar to Aaron Lun ★ 26k
Teacher to Martin Morgan 25k
Teacher to alexvpickering ▴ 110
Popular Question to k.vitting.seerup ▴ 100
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