Showing : BioStrings • reset
0
votes
5
replies
2.8k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 1 day ago Henrik Bengtsson ★ 2.4k
0
votes
3
replies
158
views
Store output of matchPWM()
biostrings Biostrings
updated 5 days ago by 65k • written 5 days ago by ▴ 70
0
votes
1
reply
139
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
2
votes
2
replies
231
views
From a DNAStringSet to a data.frame
Biostrings
6 weeks ago • updated 5 weeks ago ramiro.barrantes ▴ 10
1
vote
5
replies
435
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 weeks ago • updated 7 weeks ago Gerhard Thallinger ▴ 180
0
votes
0
replies
163
views
How to search for a string in a DNAStringSet dataset?
Biostrings
3 months ago Angela Michalichyn • 0
2
votes
6
replies
778
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
1
vote
3
replies
537
views
AAbin vs DNAbin structures
Biostrings
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
2
replies
710
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
0
votes
0
replies
364
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
14 months ago Gilles • 0
0
votes
0
replies
482
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
16 months ago Mario Dejung • 0
0
votes
0
replies
623
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
16 months ago vonSkopnik • 0
0
votes
1
reply
679
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
17 months ago • updated 16 months ago 潘晓光 • 0
0
votes
0
replies
604
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
18 months ago biong • 0
0
votes
8
replies
1.2k
views
translate errors in fastq file reading
translate biostrings Biostrings
18 months ago Brett • 0
3
votes
5
replies
1.4k
views
Biostrings multiple pattern match
pattern Biostrings
updated 19 months ago by 16k • written 19 months ago by • 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
0
votes
1
reply
737
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 20 months ago by 16k • written 2.1 years ago by • 0
1
vote
9
replies
2.4k
views
Handling DNA sequence loaded from a file
r biostrings DNAsequence
updated 23 months ago by 65k • written 8.1 years ago by ▴ 260
0
votes
2
replies
1.3k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 24 months ago by 16k • written 24 months ago by ▴ 10
0
votes
1
reply
976
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
vote
0
replies
986
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.1 years ago L ▴ 50
0
votes
4
replies
1.9k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.1 years ago by 65k • written 2.2 years ago by • 0
0
votes
0
replies
683
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.2 years ago vonSkopnik • 0
5
votes
5
replies
1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago Sam • 0
0
votes
0
replies
473
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.2 years ago Charles Plessy ▴ 180
0
votes
0
replies
657
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.2 years ago Charles Plessy ▴ 180
0
votes
2
replies
765
views
Simple subject extraction question with biostrings
Biostrings
2.3 years ago James • 0
1
vote
6
replies
1.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.3 years ago by 16k • written 2.4 years ago by ▴ 180
1
vote
2
replies
1.2k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
votes
3
replies
2.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
vote
2
replies
1.0k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.0k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.7 years ago HELEN • 0
0
votes
0
replies
765
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.7 years ago emmanuel.verde2939 • 0
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
0
votes
3
replies
969
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.1 years ago sieminsk • 0
0
votes
0
replies
927
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
3
votes
2
replies
1.8k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago Benjamin ▴ 20
0
votes
5
replies
2.5k
views
How to prevent readDNAStringSet() function from switching masked sequences (lowercase) to uppercase sequence?
biostrings mask repeatmasker DNA
updated 3.3 years ago by • 0 • written 6.5 years ago by • 0
2
votes
3
replies
1.0k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
6
votes
5
replies
1.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago Bogdan ▴ 670
1
vote
1
reply
786
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.5 years ago by ▴ 10 • written 3.6 years ago by • 0
0
votes
0
replies
681
views
vcountPDict Out-of-Memory Errors
software error Biostrings
3.6 years ago jennyl.smith12 • 0
0
votes
3
replies
1.6k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
4
replies
2.3k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.0 years ago moldach ▴ 20
1
vote
1
reply
855
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 90
0
votes
3
replies
1.3k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.0 years ago by ▴ 290 • written 4.0 years ago by ▴ 80
3
votes
1
reply
964
views
Biostrings matchPattern with lower case
biostrings
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 20
0
votes
0
replies
595
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.1 years ago multipleseqs • 0
0
votes
2
replies
981
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Awards • All
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Teacher to Gordon Smyth 50k
Popular Question to priyanka.m • 0
Locations • All
Germany, 6 minutes ago
Antwerp, Belgium, 9 minutes ago
Belgium, 25 minutes ago
Italy, 32 minutes ago
Singapore, 35 minutes ago
Traffic: 722 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