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Showing :
Biostrings
•
reset
1
vote
2
replies
219
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 11 days ago by
maltethodberg
▴ 180
2
votes
3
replies
1.2k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 8 weeks ago by
Hervé Pagès
16k • written 8 weeks ago by
Ali Osman
• 0
3
votes
4
replies
400
views
Store output of matchPWM()
biostrings
Biostrings
12 weeks ago • updated 10 weeks ago
mat149
▴ 80
0
votes
1
reply
243
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 4 months ago by
James W. MacDonald
66k • written 4 months ago by
Karen
• 0
2
votes
2
replies
491
views
From a DNAStringSet to a data.frame
Biostrings
4 months ago
ramiro.barrantes
▴ 10
1
vote
5
replies
595
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
4 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
225
views
How to search for a string in a DNAStringSet dataset?
Biostrings
6 months ago
Angela Michalichyn
• 0
2
votes
6
replies
904
views
Biostrings error at retrieving protein sequences
SequenceMatching
Biostrings
DifferentialExpression
Proteome
updated 9 months ago by
Hervé Pagès
16k • written 9 months ago by
nromerov
• 0
1
vote
3
replies
664
views
AAbin vs DNAbin structures
Biostrings
updated 10 months ago by
James W. MacDonald
66k • written 10 months ago by
rogerb
• 0
0
votes
2
replies
793
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 15 months ago by
sandmann.t
▴ 70
0
votes
0
replies
432
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
17 months ago
Gilles
• 0
0
votes
0
replies
557
views
adding peptides to a multiple sequence alignment
msa
IRanges
Biostrings
18 months ago
Mario Dejung
• 0
0
votes
0
replies
700
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment
Biostrings
19 months ago
vonSkopnik
• 0
0
votes
1
reply
759
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment
Biostrings
19 months ago
潘晓光
• 0
0
votes
0
replies
668
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity
gaps
homology
Biostrings
pairwise-alignment
20 months ago
biong
• 0
0
votes
8
replies
1.3k
views
translate errors in fastq file reading
translate
biostrings
Biostrings
21 months ago
Brett
• 0
3
votes
5
replies
1.6k
views
Biostrings multiple pattern match
pattern
Biostrings
updated 22 months ago by
Hervé Pagès
16k • written 22 months ago by
fortytwo.teacups
• 0
2
votes
2
replies
2.1k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
22 months ago
Mog
• 0
0
votes
1
reply
807
views
Using DNAStrings with Rcpp without converting to Character
Biostrings
DNAString
Rcpp
updated 23 months ago by
Hervé Pagès
16k • written 2.3 years ago by
James
• 0
0
votes
2
replies
1.5k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.2 years ago by
Hervé Pagès
16k • written 2.2 years ago by
dr
▴ 10
0
votes
1
reply
1.1k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 2.3 years ago by
Basti
▴ 780 • written 2.3 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
1.1k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments
Biostrings
Rsamtools
2.4 years ago
L
▴ 50
0
votes
4
replies
2.1k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 2.4 years ago by
James W. MacDonald
66k • written 2.4 years ago by
Eman
• 0
0
votes
0
replies
745
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.4 years ago
vonSkopnik
• 0
5
votes
5
replies
1.6k
views
Changing genetic_code_table in Biostrings
Biostrings
2.4 years ago
Sam
• 0
0
votes
0
replies
523
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.4 years ago
Charles Plessy
▴ 180
0
votes
0
replies
720
views
Pairwise alignment results with the original coordinates.
Biostrings
Alignment
2.5 years ago
Charles Plessy
▴ 180
0
votes
2
replies
847
views
Simple subject extraction question with biostrings
Biostrings
2.5 years ago
James
• 0
1
vote
6
replies
1.7k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Gerhard Thallinger
▴ 180
1
vote
2
replies
1.4k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures
Biostrings
2.7 years ago
Madza Farias-Virgens
• 0
2
votes
3
replies
2.8k
views
How to get longest isoform
GenomicFeatures
Biostrings
updated 2.7 years ago by
Hervé Pagès
16k • written 2.7 years ago by
Madza Farias-Virgens
• 0
1
vote
2
replies
1.1k
views
NAs in my txdb tx_name
GenomicFeatures
Biostrings
2.7 years ago
Madza Farias-Virgens
• 0
0
votes
4
replies
3.3k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq
rstudio
fasta
Biostrings
csv
2.9 years ago
HELEN
• 0
0
votes
0
replies
836
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation
Biostrings
3.0 years ago
emmanuel.verde2939
• 0
4
votes
9
replies
1.8k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools
Biostrings
updated 3.1 years ago by
Hervé Pagès
16k • written 3.2 years ago by
Jon Bråte
▴ 250
0
votes
0
replies
999
views
matchPattern function for multiple patterns in R
matchPattern
automatic
Biostrings
for-loop
3.3 years ago
adklts
• 0
0
votes
3
replies
1.0k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2
Gnomon
Biostrings
3.3 years ago
sieminsk
• 0
3
votes
2
replies
2.0k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData
Biostrings
3.5 years ago
Benjamin
▴ 20
2
votes
3
replies
1.1k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings
IRanges
3.6 years ago
Nicholas Cooley
• 0
6
votes
5
replies
1.8k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.7 years ago • updated 3.6 years ago
Bogdan
▴ 670
1
vote
1
reply
851
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.8 years ago by
lahuuki
▴ 10 • written 3.8 years ago by
ferbecneu
• 0
0
votes
0
replies
740
views
vcountPDict Out-of-Memory Errors
software error
Biostrings
3.8 years ago
jennyl.smith12
• 0
0
votes
3
replies
1.7k
views
What is the use of the BStringSet?
BioStrings
BStringSet
StringSet
updated 4.2 years ago by
James W. MacDonald
66k • written 4.2 years ago by
skigirl618
• 0
0
votes
4
replies
2.5k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.2 years ago
moldach
▴ 20
1
vote
1
reply
916
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings
gz
updated 4.2 years ago by
Martin Morgan
25k • written 4.2 years ago by
anand_mt
▴ 90
0
votes
3
replies
1.4k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa
Biostrings
updated 4.3 years ago by
UBod
▴ 290 • written 4.3 years ago by
Vang Le
▴ 80
3
votes
1
reply
1.1k
views
Biostrings matchPattern with lower case
biostrings
updated 4.3 years ago by
Hervé Pagès
16k • written 4.3 years ago by
story.benjamin
▴ 20
0
votes
0
replies
643
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.3 years ago
multipleseqs
• 0
0
votes
2
replies
1.1k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings
vmatchPattern
BSgenome
4.3 years ago
mb2subi
• 0
1
vote
2
replies
875
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence
human genome
GenomicAlignment
Biostrings
matchPattern
updated 4.5 years ago by
ATpoint
★ 4.2k • written 4.5 years ago by
stephen66
▴ 50
50 results • Page
1 of 1
Recent ...
Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Popular Question
to
Lluís Revilla Sancho
▴ 730
Popular Question
to
maltethodberg
▴ 180
Scholar
to
Michael Love
42k
Popular Question
to
Leonardo Collado Torres
★ 1.1k
Scholar
to
Gordon Smyth
51k
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