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Showing :
biostrings
•
reset
0
votes
5
replies
2.8k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 3 days ago
Henrik Bengtsson
★ 2.4k
0
votes
3
replies
170
views
Store output of matchPWM()
biostrings
Biostrings
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
mat149
▴ 70
0
votes
1
reply
140
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Karen
• 0
2
votes
2
replies
238
views
From a DNAStringSet to a data.frame
Biostrings
6 weeks ago
ramiro.barrantes
▴ 10
1
vote
5
replies
437
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 weeks ago • updated 7 weeks ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
165
views
How to search for a string in a DNAStringSet dataset?
Biostrings
3 months ago
Angela Michalichyn
• 0
2
votes
6
replies
780
views
Biostrings error at retrieving protein sequences
SequenceMatching
Biostrings
DifferentialExpression
Proteome
updated 7 months ago by
Hervé Pagès
16k • written 7 months ago by
nromerov
• 0
1
vote
3
replies
541
views
AAbin vs DNAbin structures
Biostrings
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
rogerb
• 0
0
votes
2
replies
712
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 12 months ago by
sandmann.t
▴ 70
0
votes
0
replies
366
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
14 months ago
Gilles
• 0
0
votes
0
replies
483
views
adding peptides to a multiple sequence alignment
msa
IRanges
Biostrings
16 months ago
Mario Dejung
• 0
0
votes
0
replies
624
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment
Biostrings
16 months ago
vonSkopnik
• 0
0
votes
1
reply
680
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment
Biostrings
17 months ago
潘晓光
• 0
0
votes
0
replies
605
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
Hervé Pagès
16k • written 19 months ago by
fortytwo.teacups
• 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
738
views
Using DNAStrings with Rcpp without converting to Character
Biostrings
DNAString
Rcpp
updated 20 months ago by
Hervé Pagès
16k • written 2.1 years ago by
James
• 0
1
vote
9
replies
2.4k
views
Handling DNA sequence loaded from a file
r
biostrings
DNAsequence
updated 23 months ago by
James W. MacDonald
65k • written 8.1 years ago by
Agaz Hussain Wani
▴ 260
0
votes
2
replies
1.3k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 24 months ago by
Hervé Pagès
16k • written 24 months ago by
dr
▴ 10
0
votes
1
reply
979
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
989
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 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Eman
• 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
768
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
Hervé Pagès
16k • written 2.4 years ago by
Gerhard Thallinger
▴ 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
Hervé Pagès
16k • written 2.5 years ago by
Madza Farias-Virgens
• 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
767
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
Hervé Pagès
16k • written 3.0 years ago by
Jon Bråte
▴ 250
0
votes
3
replies
971
views
DESeq2 - extracting results - Gnomon gene model
DESeq2
Gnomon
Biostrings
3.1 years ago
sieminsk
• 0
0
votes
0
replies
928
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
ivantsers
• 0 • written 6.5 years ago by
beausoleilmo
• 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
lahuuki
▴ 10 • written 3.6 years ago by
ferbecneu
• 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
James W. MacDonald
65k • written 3.9 years ago by
skigirl618
• 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
856
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings
gz
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
anand_mt
▴ 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
UBod
▴ 290 • written 4.0 years ago by
Vang Le
▴ 80
3
votes
1
reply
967
views
Biostrings matchPattern with lower case
biostrings
updated 4.1 years ago by
Hervé Pagès
16k • written 4.1 years ago by
story.benjamin
▴ 20
0
votes
0
replies
595
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.1 years ago
multipleseqs
• 0
0
votes
2
replies
982
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: EGSEA usage with microarray data (with vooma)?
by
Chris
• 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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