Showing : biostrings • reset
8
votes
3
replies
3.3k
views
Algorithm description for matchPWM (Biostrings)
biostrings matchPWM
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 370
6
votes
11
replies
3.0k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 9.5 years ago by ▴ 180 • written 9.5 years ago by ▴ 40
6
votes
5
replies
1.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.5 years ago Bogdan ▴ 670
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 16k • written 7.5 years ago by ▴ 70
6
votes
8
replies
2.8k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 80
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
8.0 years ago likeeatingpizza ▴ 10
5
votes
20
replies
3.1k
views
matching of AAStringSet vs. another AAStringSet
biostrings AAStringset
7.5 years ago • updated 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 8.8 years ago by ▴ 50 • written 8.8 years ago by • 0
5
votes
8
replies
6.1k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
9.3 years ago ben.ward ▴ 30
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.1 years ago by 16k • written 7.1 years ago by ▴ 70
5
votes
1
reply
1.7k
views
Chromosome position to nucleotide - Biostrings?
biostrings
updated 9.6 years ago by ★ 1.3k • written 9.6 years ago by ▴ 120
5
votes
1
reply
3.1k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 4.4 years ago by ▴ 100 • written 4.4 years ago by ▴ 20
5
votes
5
replies
1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago Sam • 0
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 6.4 years ago by ▴ 150 • written 6.4 years ago by • 0
4
votes
7
replies
1.6k
views
how to catch an error when using subseq() in vectorized way
biostrings subseq
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 20
4
votes
2
replies
2.0k
views
Biostrings regex matching
Biostrings
updated 4.9 years ago by 16k • written 5.0 years ago by ▴ 160
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
5
replies
1.2k
views
XStringSet operations discard names - how to address?
biostrings
updated 8.0 years ago by 16k • written 8.0 years ago by • 0
4
votes
1
reply
1.0k
views
IRanges, Partitioning by End function not found.
IRanges Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 30
4
votes
7
replies
2.2k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 20
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 3.0 years ago by ▴ 250
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 16k • written 9.5 years ago by ▴ 120
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 25k • written 8.8 years ago by • 0
3
votes
2
replies
1.4k
views
pairwiseAlignments coordinate mapping?
biostrings pairwisealignment
updated 8.0 years ago by 16k • written 8.0 years ago by ★ 13k
3
votes
2
replies
4.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 10
3
votes
3
replies
1.4k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 5.3 years ago by ★ 11k • written 5.3 years ago by ▴ 120
3
votes
4
replies
275
views
Store output of matchPWM()
biostrings Biostrings
17 days ago • updated 4 days ago mat149 ▴ 70
3
votes
2
replies
1.3k
views
Get a complete view of a long DNA sequence of a Biostrings object in R
biostrings subsetting View dnastring dnaseq
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
3
votes
5
replies
1.5k
views
Biostrings multiple pattern match
pattern Biostrings
updated 19 months ago by 16k • written 19 months ago by • 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
3
votes
3
replies
1.6k
views
Reading large DNA alignments and keeping polymorphic sites
sequence alignment biostrings
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 30
3
votes
4
replies
1.4k
views
findComplementedPalindromes function is not finding all complementary palindromes
Biostrings
updated 9.4 years ago by 16k • written 9.5 years ago by • 0
3
votes
1
reply
982
views
Biostrings matchPattern with lower case
biostrings
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 20
2
votes
4
replies
1.2k
views
Ranges on AAStrings
AAString Views Biostrings
7.2 years ago tobias.kockmann ▴ 20
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ★ 1.5k
2
votes
2
replies
1.1k
views
Creating a Biostrings PDict object from amino-acid sequences
biostrings pdict
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 110
2
votes
4
replies
4.3k
views
What is the best way to subset a DNAStringSet by a GRange ?
bioconductor biostrings granges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by • 0
2
votes
2
replies
1.0k
views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 20
2
votes
1
reply
1.1k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 40
2
votes
2
replies
906
views
vcountPDict fails on PDict
Biostrings
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 160
2
votes
2
replies
949
views
Trim a variable number of bases off read, depending on read length
Biostrings
8.2 years ago knaxerova ▴ 10
2
votes
2
replies
1.2k
views
Exclude masked rownames in DNAMultipleAlignments
multiple sequences masks rowmask rownames biostrings
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 30
2
votes
5
replies
1.6k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by • 0
2
votes
1
reply
955
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 6.3 years ago by 3.9k • written 6.3 years ago by ▴ 10
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
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
2
votes
2
replies
2.3k
views
msa: How to obtain a subset of an alignment
msa Biostrings MultipleAlignment
updated 6.7 years ago by ▴ 290 • written 6.7 years ago by ▴ 10
2
votes
1
reply
1.0k
views
Error in score() function on pairwiseAlignment()
biostrings pairwisealignment
updated 8.0 years ago by 3.9k • written 8.0 years ago by • 0
2
votes
3
replies
1.8k
views
Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher DNA biostrings
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by • 0
2
votes
2
replies
1.9k
views
How to combine sequences from different stringsets?
biostrings decipher
updated 6.3 years ago by ★ 6.5k • written 6.3 years ago by • 0
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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