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Showing :
BioStrings
•
reset
5
votes
20
replies
3.1k
views
matching of AAStringSet vs. another AAStringSet
biostrings
AAStringset
7.4 years ago
tobias.kockmann
▴ 20
5
votes
15
replies
3.2k
views
problem with QDNAseq's createBins for new BSgenome package
bsgenome
biostrings
qdnaseq
pfalciparum
updated 8.7 years ago by
ilari.scheinin
▴ 50 • written 8.7 years ago by
penington.j
• 0
0
votes
14
replies
3.5k
views
Trimming of partial adaptor sequences
Sequencing
Cancer
Biostrings
Sequencing
Cancer
Biostrings
10.8 years ago
Taylor, Sean D
▴ 250
4
votes
13
replies
4.4k
views
How to create an output file with sequence ID's from multiple BLAST result using blastSequences in "Biostrings"
annotation
blast
biostrings
updated 8.8 years ago by
Martin Morgan
25k • written 8.8 years ago by
Mathilde
• 0
0
votes
13
replies
2.5k
views
forge BSgenome data package
BSgenome
Biostrings
BSgenome
BSgenome
Biostrings
BSgenome
updated 13.3 years ago by
Hervé Pagès
16k • written 13.3 years ago by
Steve Shen
▴ 330
0
votes
13
replies
1.9k
views
PWMscoreStartingAt and ambiguous subject seqs
Cancer
Biostrings
GLAD
Cancer
Biostrings
GLAD
updated 12.0 years ago by
Hervé Pagès
16k • written 12.0 years ago by
Janet Young
▴ 740
0
votes
12
replies
1.5k
views
DNAString ("GC") -- error in nchar?
Biostrings
Biostrings
updated 16.6 years ago by
Martin Morgan
25k • written 16.6 years ago by
Paul Shannon
★ 1.1k
6
votes
11
replies
3.0k
views
Comparing read sequence back to reference sequence
bam
indel
genomicalignments
biostrings
updated 9.5 years ago by
Nathaniel Hayden
▴ 180 • written 9.5 years ago by
Stefanie Tauber
▴ 40
0
votes
11
replies
5.7k
views
Biostring: print sequence alignment to file
Alignment
Biostrings
Alignment
Biostrings
updated 12.1 years ago by
Thomas Girke
★ 1.7k • written 12.1 years ago by
Martin Preusse
▴ 100
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 2.9 years ago by
Jon Bråte
▴ 250
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
9
replies
1.9k
views
Mapping microarray probes to the genome using findOverlaps
Microarray
Alignment
Annotation
zebrafish
probe
Biostrings
GenomicFeatures
Microarray
updated 13.2 years ago by
Sean Davis
21k • written 13.2 years ago by
Hervé Pagès
16k
1
vote
9
replies
2.8k
views
BLAST search sequence for species ID from R?
Biostrings
PROcess
Biostrings
PROcess
updated 14.4 years ago by
Michael Dondrup
▴ 550 • written 14.4 years ago by
jos matejus
▴ 40
0
votes
9
replies
1.9k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation
Cancer
Yeast
annotate
Biostrings
VariantAnnotation
VariantAnnotation
updated 10.3 years ago by
Hervé Pagès
16k • written 10.3 years ago by
Janet Young
▴ 740
0
votes
9
replies
1.7k
views
Error with unique
Biostrings
Biostrings
updated 14.1 years ago by
Sean Davis
21k • written 14.1 years ago by
Erik Wright
▴ 210
0
votes
8
replies
1.2k
views
translate errors in fastq file reading
translate
biostrings
Biostrings
18 months ago
Brett
• 0
6
votes
8
replies
2.8k
views
Ranges from a fasta file
biostrings
fasta
genomicranges
granges
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
Konstantinos Yeles
▴ 80
5
votes
8
replies
6.1k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam
sam
alignment
biostrings
9.2 years ago
ben.ward
▴ 30
2
votes
8
replies
2.0k
views
CAGEr BAM files size issue
CAGEr
BAM
software error
R
biostrings
updated 6.7 years ago by
Charles Plessy
▴ 180 • written 6.8 years ago by
orzechowska.mag
▴ 10
4
votes
7
replies
1.6k
views
how to catch an error when using subseq() in vectorized way
biostrings
subseq
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
tobias.kockmann
▴ 20
5
votes
7
replies
1.7k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R
decipher
biostrings
updated 6.3 years ago by
Erik Wright
▴ 150 • written 6.3 years ago by
reubenmcgregor88
• 0
0
votes
7
replies
1.7k
views
Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings
GenomicFeatures
Biostrings
GenomicFeatures
updated 13.2 years ago by
Michael Lawrence
★ 11k • written 13.2 years ago by
Hervé Pagès
16k
4
votes
7
replies
1.5k
views
Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
Biostrings
7.8 years ago
matt.chambers42
▴ 10
4
votes
7
replies
2.2k
views
IRanges/ShortRead causing crash?
iranges
shortread
Biostrings
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
pavitrarc
▴ 20
1
vote
7
replies
2.5k
views
Mapping Probes to a Genome
BSgenome
biostrings
probe mapping
updated 7.0 years ago by
holgerbrandl
▴ 10 • written 7.7 years ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
2.4k
views
Biostrings pairwiseAligment() output shorter than source sequence
Biostrings
8.7 years ago
jean.peccoud
• 0
0
votes
6
replies
1.4k
views
SNPcounts error in SNPlocs.Hsapiens.dbSNP.20110815_0.99.3 (i.e., my attempt to update SNPlocs to dbSNP build 134)
Regression
SNPlocs
Biostrings
Regression
SNPlocs
Biostrings
updated 12.6 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.6 years ago by
Tim Triche
★ 4.2k
0
votes
6
replies
1.8k
views
Gviz/Biostrings memory issue?
gviz
biostrings
7.4 years ago
stianlagstad
▴ 90
0
votes
6
replies
1.1k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair
BSgenome
Biostrings
BSgenome.Hsapiens.UCSC.hg19
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
svetlana.gorokhova
• 0
0
votes
6
replies
2.0k
views
Biostring: print sequence alignment to file
Alignment
Cancer
Biostrings
Alignment
Cancer
Biostrings
updated 11.8 years ago by
Martin Preusse
▴ 100 • written 11.8 years ago by
Hervé Pagès
16k
2
votes
6
replies
778
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
6
votes
6
replies
2.5k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges
biostrings
bsapply
BSgenome
updated 7.5 years ago by
Hervé Pagès
16k • written 7.5 years ago by
jma1991
▴ 70
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
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
4
votes
5
replies
1.2k
views
XStringSet operations discard names - how to address?
biostrings
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
nicholasbauer
• 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
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
5
replies
1.3k
views
Error Raised When Trying To Use pileup()
hilbertvis
rsamtools
shortread
biostrings
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
travis.m.couture
• 0
0
votes
5
replies
1.9k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment
Biostrings
Alignment
Biostrings
13.9 years ago • updated 13.8 years ago
Coghlan, Avril
▴ 190
5
votes
5
replies
1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago
Sam
• 0
0
votes
5
replies
1.2k
views
Biostrings C interface :: example not compiling
Biostrings
Biostrings
updated 14.1 years ago by
Charles Berry
▴ 290 • written 14.1 years ago by
Erik Wright
▴ 210
6
votes
5
replies
1.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago
Bogdan
▴ 670
0
votes
5
replies
1.4k
views
Splitting a fasta file based on specific Amino acid for plotting
iranges
biostrings
fasta
protein
readaastringset
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
5
replies
1.4k
views
from TF DNA binding motif to downstream genes?
Transcription
Biostrings
Transcription
Biostrings
updated 14.3 years ago by
Patrick Aboyoun
★ 1.6k • written 14.3 years ago by
Paul Shannon
★ 1.1k
4
votes
5
replies
2.6k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings
pairwiseAlignment
updated 9.5 years ago by
Hervé Pagès
16k • written 9.5 years ago by
branislav misovic
▴ 120
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
0
votes
5
replies
2.5k
views
Fisher-Yates algorithm for DNA shuffling ?
Biostrings
Biostrings
updated 14.9 years ago by
Hervé Pagès
16k • written 14.9 years ago by
Robert Castelo
★ 3.3k
2
votes
5
replies
1.6k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r
decipher
biostrings
updated 6.3 years ago by
Erik Wright
▴ 150 • written 6.3 years ago by
reubenmcgregor88
• 0
2
votes
4
replies
4.2k
views
What is the best way to subset a DNAStringSet by a GRange ?
bioconductor
biostrings
granges
updated 7.1 years ago by
Michael Lawrence
★ 11k • written 7.1 years ago by
reuscher.stefan
• 0
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings
shortread
updated 7.1 years ago by
Hervé Pagès
16k • written 7.1 years ago by
jma1991
▴ 70
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
41k
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: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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