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Biostrings
•
reset
1
vote
3
replies
298
views
readDNAStringSet with non DNA characters
Biostrings
5 weeks ago
biomiha
▴ 20
0
votes
2
replies
214
views
Create consensusMatrix for codon bases
Biostrings
updated 10 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
Hassan
• 0
1
vote
7
replies
2.5k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 6 months ago by
stenlana035
• 0 • written 3.9 years ago by
Gerhard Thallinger
▴ 180
4
votes
9
replies
2.8k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker
GenomeInfoDb
GenomicFeatures
Biostrings
gDNAx
updated 9 months ago by
Robert Castelo
★ 3.4k • written 10 months ago by
rohitsatyam102
▴ 20
0
votes
1
reply
335
views
Matching patterns in an AAStringset
Biostrings
updated 10 months ago by
Aidan
▴ 70 • written 10 months ago by
Cédric
• 0
1
vote
4
replies
991
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges
Biostrings
S4Vectors
written 12 months ago by
Christine Jones
• 0
1
vote
3
replies
910
views
How to reverse complement some elements of a DNAStringSet
biostr
Biostrings
updated 7 months ago by
shrill.asp.tufl
• 0 • written 12 months ago by
Christine Jones
• 0
1
vote
2
replies
730
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata
Biostrings
updated 10 months ago by
Aidan
▴ 70 • written 12 months ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
739
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings
aminoacid
motifbreakR
written 14 months ago by
wilson_ava
• 0
0
votes
1
reply
1.2k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings
packageinstallation
updated 13 months ago by
Aidan
▴ 70 • written 13 months ago by
semra
• 0
4
votes
2
replies
983
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 15 months ago by
maltethodberg
▴ 180
2
votes
3
replies
1.8k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 17 months ago by
Hervé Pagès
16k • written 17 months ago by
Ali Osman
• 0
3
votes
4
replies
905
views
Store output of matchPWM()
biostrings
Biostrings
18 months ago • updated 17 months ago
mat149
▴ 80
0
votes
1
reply
668
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Karen
• 0
2
votes
2
replies
2.2k
views
From a DNAStringSet to a data.frame
Biostrings
19 months ago
ramiro.barrantes
▴ 10
1
vote
5
replies
1.2k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
19 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
497
views
How to search for a string in a DNAStringSet dataset?
Biostrings
21 months ago
Angela Michalichyn
• 0
2
votes
6
replies
1.5k
views
Biostrings error at retrieving protein sequences
SequenceMatching
Biostrings
DifferentialExpression
Proteome
updated 2.1 years ago by
Hervé Pagès
16k • written 2.1 years ago by
nromerov
• 0
1
vote
3
replies
1.2k
views
AAbin vs DNAbin structures
Biostrings
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
rogerb
• 0
0
votes
2
replies
1.3k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 2.5 years ago by
sandmann.t
▴ 70
0
votes
0
replies
757
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.7 years ago
Gilles
• 0
0
votes
0
replies
934
views
adding peptides to a multiple sequence alignment
msa
IRanges
Biostrings
2.8 years ago
Mario Dejung
• 0
0
votes
0
replies
1.1k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment
Biostrings
2.8 years ago
vonSkopnik
• 0
0
votes
2
replies
1.3k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment
Biostrings
updated 12 months ago by
rohitsatyam102
▴ 20 • written 2.9 years ago by
潘晓光
• 0
0
votes
0
replies
1.1k
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity
gaps
homology
Biostrings
pairwise-alignment
3.0 years ago
biong
• 0
0
votes
8
replies
2.2k
views
translate errors in fastq file reading
translate
biostrings
Biostrings
3.0 years ago
Brett
• 0
3
votes
5
replies
2.3k
views
Biostrings multiple pattern match
pattern
Biostrings
updated 3.1 years ago by
Hervé Pagès
16k • written 3.1 years ago by
fortytwo.teacups
• 0
2
votes
2
replies
3.3k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
3.1 years ago
Mog
• 0
0
votes
1
reply
1.3k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings
DNAString
Rcpp
updated 3.2 years ago by
Hervé Pagès
16k • written 3.5 years ago by
James
• 0
0
votes
2
replies
2.4k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.4 years ago by
Hervé Pagès
16k • written 3.5 years ago by
dr
▴ 10
0
votes
1
reply
1.7k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
1.5k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments
Biostrings
Rsamtools
3.6 years ago
L
▴ 50
0
votes
4
replies
3.0k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
Eman
• 0
0
votes
0
replies
1.0k
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.7 years ago
vonSkopnik
• 0
5
votes
5
replies
2.4k
views
Changing genetic_code_table in Biostrings
Biostrings
3.7 years ago
Sam
• 0
0
votes
0
replies
792
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.7 years ago
Charles Plessy
▴ 180
0
votes
0
replies
1.0k
views
Pairwise alignment results with the original coordinates.
Biostrings
Alignment
3.7 years ago
Charles Plessy
▴ 180
0
votes
2
replies
1.3k
views
Simple subject extraction question with biostrings
Biostrings
3.7 years ago
James
• 0
1
vote
2
replies
1.9k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures
Biostrings
3.9 years ago
Madza Farias-Virgens
• 0
2
votes
3
replies
3.8k
views
How to get longest isoform
GenomicFeatures
Biostrings
updated 3.9 years ago by
Hervé Pagès
16k • written 3.9 years ago by
Madza Farias-Virgens
• 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures
Biostrings
3.9 years ago
Madza Farias-Virgens
• 0
0
votes
4
replies
4.5k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq
rstudio
fasta
Biostrings
csv
4.2 years ago
HELEN
• 0
0
votes
0
replies
1.2k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation
Biostrings
4.2 years ago
emmanuel.verde2939
• 0
4
votes
9
replies
2.6k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools
Biostrings
updated 4.4 years ago by
Hervé Pagès
16k • written 4.4 years ago by
Jon Bråte
▴ 270
0
votes
0
replies
1.4k
views
matchPattern function for multiple patterns in R
matchPattern
automatic
Biostrings
for-loop
4.6 years ago
adklts
• 0
0
votes
3
replies
1.5k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2
Gnomon
Biostrings
4.6 years ago
sieminsk
• 0
3
votes
2
replies
2.8k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData
Biostrings
4.8 years ago
Benjamin
▴ 20
2
votes
3
replies
1.6k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings
IRanges
4.9 years ago
Nicholas Cooley
• 0
6
votes
5
replies
2.8k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.9 years ago
Bogdan
▴ 670
1
vote
1
reply
1.2k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.0 years ago by
lahuuki
▴ 10 • written 5.0 years ago by
ferbecneu
• 0
292 results • Page
1 of 6
Recent ...
Replies
Comment: Interpretation of output of AffyRNAdeg and hist commands
by
debasainalsa
• 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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