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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
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
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
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
0
votes
4
replies
1.4k
views
R: R: R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)
miRNA
Biophysics
Biostrings
biomaRt
miRNA
Biophysics
Biostrings
biomaRt
14.9 years ago
mauede@alice.it
▴ 870
0
votes
4
replies
1.3k
views
BSgenome.Osativa.MSU.MSU7 Oryza sativa
bsgenome
biostrings
7.9 years ago
Didi
▴ 10
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
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
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
3
replies
1.8k
views
Problem with Biostrings
Biostrings
Biostrings
12.7 years ago
Guido Leoni
▴ 200
0
votes
4
replies
1.6k
views
advice on Biostrings
Biostrings
Biostrings
updated 18.2 years ago by
Martin Morgan
25k • written 18.2 years ago by
Rafael A. Irizarry
★ 2.3k
8
votes
3
replies
3.3k
views
Algorithm description for matchPWM (Biostrings)
biostrings
matchPWM
updated 9.6 years ago by
Hervé Pagès
16k • written 9.6 years ago by
Yue Li
▴ 370
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
1
vote
7
replies
2.4k
views
Biostrings pairwiseAligment() output shorter than source sequence
Biostrings
8.7 years ago
jean.peccoud
• 0
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
James W. MacDonald
65k • written 2.1 years ago by
Eman
• 0
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
5
votes
5
replies
1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago
Sam
• 0
0
votes
2
replies
1.7k
views
Solexa fastq files and BLAT
Cancer
Biostrings
ShortRead
Cancer
Biostrings
ShortRead
updated 5.3 years ago by
Bioconductor Community
0 • written 15.3 years ago by
Daniel Brewer
★ 1.9k
0
votes
2
replies
1.2k
views
Human reference primary assembly and masking using BioStrings and BSgenome
biostrings
R
bsgenome
6.9 years ago
rockyb
• 0
0
votes
4
replies
3.7k
views
Retrieving specific sequences from a fastq
shortread
biostrings
5.6 years ago
ferbecneu
• 0
1
vote
5
replies
432
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 weeks ago • updated 6 weeks ago
Gerhard Thallinger
▴ 180
0
votes
3
replies
1.2k
views
matchPWM on DNAStringSet rather than just one sequence?
biostrings
7.9 years ago
Jake
▴ 90
0
votes
2
replies
4.9k
views
Possible bug in Biostrings::readAAStringSet
bug
biostrings
readAAStringSet
updated 7.6 years ago by
Guangchuang Yu
★ 1.2k • written 7.6 years ago by
asis.hallab
• 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
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
0
votes
3
replies
4.8k
views
Biostrings character vector conversion
biostrings
7.9 years ago
ribioinfo
▴ 100
0
votes
2
replies
1.3k
views
the same problem happened
Biostrings
Biostrings
updated 12.6 years ago by
Sean Davis
21k • written 12.6 years ago by
wang peter
★ 2.0k
1
vote
2
replies
801
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence
human genome
GenomicAlignment
Biostrings
matchPattern
updated 4.3 years ago by
ATpoint
★ 4.1k • written 4.3 years ago by
stephen66
▴ 50
0
votes
2
replies
2.1k
views
PWM matching using matchPWM in Biostrings
Transcription
BSgenome
Biostrings
BSgenome
Transcription
BSgenome
Biostrings
BSgenome
updated 15.0 years ago by
Patrick Aboyoun
★ 1.6k • written 15.0 years ago by
Kristoffer Rigbolt
▴ 10
2
votes
6
replies
774
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
2
votes
2
replies
938
views
Trim a variable number of bases off read, depending on read length
Biostrings
8.1 years ago
knaxerova
▴ 10
0
votes
7
replies
1.7k
views
Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings
GenomicFeatures
Biostrings
GenomicFeatures
updated 13.1 years ago by
Michael Lawrence
★ 11k • written 13.2 years ago by
Hervé Pagès
16k
2
votes
4
replies
1.3k
views
vcountPattern for Pattern Contained within or Containing Subject
biostrings
countpattern
8.5 years ago
Dario Strbenac
★ 1.5k
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
2
votes
2
replies
1.8k
views
BLAST export library 'annotate'
blast
annotate
biostrings
export
fasta
9.5 years ago
b.stielow
• 0
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
2
replies
6.4k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP
Sequencing
Coverage
Alignment
Cancer
Biostrings
PROcess
IRanges
GenomicRanges
SNP
updated 10.5 years ago by
Michael Lawrence
★ 11k • written 10.5 years ago by
Hervé Pagès
16k
0
votes
2
replies
1.2k
views
how to use writeFASTA in modality "append"
Transcription
miRNA
Biostrings
Transcription
miRNA
Biostrings
updated 14.8 years ago by
Hervé Pagès
16k • written 14.8 years ago by
mauede@alice.it
▴ 870
0
votes
2
replies
858
views
OS X 10.7.x "Lion"
Biostrings
Biostrings
updated 12.2 years ago by
delhomme@embl.de
★ 1.2k • written 12.2 years ago by
Tom Keller
▴ 70
2
votes
3
replies
1.2k
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment
biostrings
8.6 years ago
vincent.plagnol
▴ 10
0
votes
4
replies
1.8k
views
BLAST E-value
Biostrings
Biostrings
updated 14.2 years ago by
Richard Friedman
★ 2.0k • written 14.2 years ago by
Alla Bulashevska
▴ 60
0
votes
4
replies
2.8k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago
Henrik Bengtsson
★ 2.4k
0
votes
2
replies
1.6k
views
sequence search using a position weight matrix?
Biostrings
cosmo
Biostrings
cosmo
updated 16.6 years ago by
Hervé Pagès
16k • written 16.6 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
1.2k
views
Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment
Cancer
Biostrings
IRanges
Alignment
Cancer
Biostrings
IRanges
updated 10.6 years ago by
Marcin Imielinski
▴ 30 • written 10.6 years ago by
Hervé Pagès
16k
0
votes
4
replies
2.1k
views
BSgenomes vs ENSEMBL
Transcription
Annotation
BSgenome
annotate
Biostrings
BSgenome
Transcription
Annotation
updated 15.6 years ago by
Hervé Pagès
16k • written 15.6 years ago by
Guido Hooiveld
★ 3.9k
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings
coverage
rle
iranges
7.9 years ago
likeeatingpizza
▴ 10
0
votes
5
replies
1.9k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment
Biostrings
Alignment
Biostrings
13.8 years ago
Coghlan, Avril
▴ 190
0
votes
3
replies
900
views
[biocpkgs] suggestions on package matchprobes
Cancer
Biostrings
Cancer
Biostrings
updated 17.6 years ago by
Xinxia Peng
▴ 120 • written 17.7 years ago by
rgentleman
★ 5.5k
0
votes
2
replies
1.6k
views
inconsistent pairwiseAlignment behaviour (Biostrings) with multiple alignments with identical scores
biostrings
pairwisealignment
8.6 years ago
vincent.plagnol
▴ 10
0
votes
1
reply
1.2k
views
R: R: R: R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)
miRNA
Biophysics
GO
Homo sapiens
Biostrings
biomaRt
miRNA
Biophysics
GO
Homo sapiens
updated 14.9 years ago by
Sean Davis
21k • written 14.9 years ago by
mauede@alice.it
▴ 870
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Comment: fgsea significant result
by
Chris
• 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
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Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
package goseq seems to be not available on the latest version of R
Print Differentially Expressed Exons From Dexseq Results
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