Showing : biostrings • reset
1
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7
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2.3k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 5 weeks ago by • 0 • written 3.4 years ago by ▴ 180
4
votes
9
replies
2.4k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 3 months ago by ★ 3.4k • written 4 months ago by ▴ 20
0
votes
1
reply
240
views
Matching patterns in an AAStringset
Biostrings
updated 5 months ago by ▴ 60 • written 5 months ago by • 0
1
vote
4
replies
847
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 6 months ago by • 0
1
vote
3
replies
730
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
updated 7 weeks ago by • 0 • written 7 months ago by • 0
1
vote
2
replies
603
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 4 months ago by ▴ 60 • written 7 months ago by ▴ 180
0
votes
2
replies
630
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 8 months ago by • 0
0
votes
1
reply
1.0k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 8 months ago by ▴ 60 • written 8 months ago by • 0
4
votes
2
replies
826
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 10 months ago by ▴ 180
2
votes
3
replies
1.6k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 11 months ago by 16k • written 11 months ago by • 0
3
votes
4
replies
773
views
Store output of matchPWM()
biostrings Biostrings
12 months ago mat149 ▴ 80
0
votes
1
reply
547
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 13 months ago by 68k • written 13 months ago by • 0
2
votes
2
replies
1.9k
views
From a DNAStringSet to a data.frame
Biostrings
13 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
996
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
14 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
414
views
How to search for a string in a DNAStringSet dataset?
Biostrings
16 months ago Angela Michalichyn • 0
2
votes
6
replies
1.3k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 19 months ago by 16k • written 19 months ago by • 0
1
vote
3
replies
1.1k
views
AAbin vs DNAbin structures
Biostrings
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
2
replies
1.1k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.0 years ago by ▴ 70
0
votes
0
replies
672
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.2 years ago Gilles • 0
0
votes
0
replies
812
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.3 years ago Mario Dejung • 0
0
votes
0
replies
975
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.4 years ago vonSkopnik • 0
0
votes
2
replies
1.1k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 7 months ago by ▴ 20 • written 2.4 years ago by • 0
0
votes
0
replies
966
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.5 years ago biong • 0
0
votes
8
replies
1.9k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.6 years ago Brett • 0
3
votes
5
replies
2.1k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
2
votes
2
replies
3.0k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.6 years ago Mog • 0
0
votes
1
reply
1.1k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.7 years ago by 16k • written 3.1 years ago by • 0
0
votes
2
replies
2.2k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.5k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
1
vote
0
replies
1.4k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.2 years ago L ▴ 50
0
votes
4
replies
2.8k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
0
replies
961
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.2 years ago vonSkopnik • 0
5
votes
5
replies
2.1k
views
Changing genetic_code_table in Biostrings
Biostrings
3.2 years ago Sam • 0
0
votes
0
replies
717
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.2 years ago Charles Plessy ▴ 180
0
votes
0
replies
928
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.3 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.2k
views
Simple subject extraction question with biostrings
Biostrings
3.3 years ago James • 0
1
vote
2
replies
1.8k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.5 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
1
vote
2
replies
1.4k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.5 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.2k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.7 years ago HELEN • 0
0
votes
0
replies
1.1k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.8 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.3k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.9 years ago by 16k • written 4.0 years ago by ▴ 270
0
votes
0
replies
1.2k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.1 years ago adklts • 0
0
votes
3
replies
1.3k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.2 years ago • updated 4.1 years ago sieminsk • 0
3
votes
2
replies
2.7k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.3 years ago Benjamin ▴ 20
2
votes
3
replies
1.4k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.4 years ago Nicholas Cooley • 0
6
votes
5
replies
2.5k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.5 years ago Bogdan ▴ 670
1
vote
1
reply
1.1k
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
0
votes
0
replies
952
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.6 years ago JennyS • 0
0
votes
3
replies
2.2k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
50 results • Page 1 of 1
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Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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