Showing : Biostrings • reset
0
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3
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334
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Create consensusMatrix for codon bases
Biostrings
updated 14 days ago by ★ 4.0k • written 3 months ago by • 0
1
vote
3
replies
412
views
readDNAStringSet with non DNA characters
Biostrings
11 weeks ago biomiha ▴ 20
1
vote
7
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2.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 8 months ago by • 0 • written 4.0 years ago by ▴ 180
4
votes
9
replies
3.0k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 10 months ago by ★ 3.4k • written 11 months ago by ▴ 20
0
votes
1
reply
373
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Matching patterns in an AAStringset
Biostrings
updated 12 months ago by ▴ 70 • written 12 months ago by • 0
1
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4
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1.0k
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 13 months ago by • 0
1
vote
4
replies
1.0k
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 13 months ago by • 0
1
vote
2
replies
773
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 11 months ago by ▴ 70 • written 13 months ago by ▴ 180
0
votes
2
replies
774
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 15 months ago by • 0
0
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1
reply
1.4k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
4
votes
2
replies
1.0k
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 16 months ago by ▴ 180
2
votes
3
replies
1.8k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 18 months ago by 16k • written 18 months ago by • 0
3
votes
4
replies
956
views
Store output of matchPWM()
biostrings Biostrings
19 months ago mat149 ▴ 80
0
votes
1
reply
690
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 20 months ago by 68k • written 20 months ago by • 0
2
votes
2
replies
2.3k
views
From a DNAStringSet to a data.frame
Biostrings
20 months ago ramiro.barrantes ▴ 10
1
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5
replies
1.3k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
21 months ago • updated 20 months ago Gerhard Thallinger ▴ 180
0
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0
replies
526
views
How to search for a string in a DNAStringSet dataset?
Biostrings
22 months ago Angela Michalichyn • 0
2
votes
6
replies
1.6k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
1
vote
3
replies
1.3k
views
AAbin vs DNAbin structures
Biostrings
updated 2.2 years ago by 68k • written 2.3 years ago by • 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 2.6 years ago by ▴ 70
0
votes
0
replies
777
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.8 years ago Gilles • 0
0
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0
replies
965
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.9 years ago Mario Dejung • 0
0
votes
0
replies
1.1k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.9 years ago vonSkopnik • 0
0
votes
2
replies
1.3k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 13 months ago by ▴ 20 • written 3.0 years ago by • 0
0
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0
replies
1.1k
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
3.1 years ago biong • 0
0
votes
8
replies
2.2k
views
translate errors in fastq file reading
translate biostrings Biostrings
3.1 years ago Brett • 0
3
votes
5
replies
2.3k
views
Biostrings multiple pattern match
pattern Biostrings
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
2
votes
2
replies
3.4k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.2 years ago Mog • 0
0
votes
1
reply
1.3k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 3.3 years ago by 16k • written 3.7 years ago by • 0
0
votes
2
replies
2.4k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.6 years ago by 16k • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.7k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.6 years ago by ▴ 780 • written 3.7 years ago by • 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
3.7 years ago L ▴ 50
0
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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 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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0
replies
1.0k
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.8 years ago vonSkopnik • 0
5
votes
5
replies
2.4k
views
Changing genetic_code_table in Biostrings
Biostrings
3.8 years ago Sam • 0
0
votes
0
replies
815
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.8 years ago Charles Plessy ▴ 180
0
votes
0
replies
1.1k
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.8 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.3k
views
Simple subject extraction question with biostrings
Biostrings
3.9 years ago James • 0
1
vote
2
replies
2.0k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.1 years ago • updated 4.0 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.9k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.1 years ago by 16k • written 4.1 years ago by • 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.1 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.6k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
4.3 years ago HELEN • 0
0
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0
replies
1.2k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
4.3 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 270
0
votes
0
replies
1.4k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.7 years ago adklts • 0
0
votes
3
replies
1.5k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.7 years ago sieminsk • 0
3
votes
2
replies
2.9k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.9 years ago Benjamin ▴ 20
2
votes
3
replies
1.7k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
5.0 years ago Nicholas Cooley • 0
6
votes
5
replies
2.8k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
5.0 years ago Bogdan ▴ 670
1
vote
1
reply
1.2k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.1 years ago by ▴ 10 • written 5.2 years ago by • 0
292 results • Page 1 of 6
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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