Showing : biostrings • reset
4
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9
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2.0k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 3 days ago by ★ 3.4k • written 5 weeks ago by ▴ 20
0
votes
1
reply
167
views
Matching patterns in an AAStringset
Biostrings
updated 6 weeks ago by ▴ 60 • written 6 weeks ago by • 0
1
vote
4
replies
695
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 3 months ago by • 0
1
vote
3
replies
380
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 3 months ago by • 0
1
vote
2
replies
472
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 5 weeks ago by ▴ 60 • written 3 months ago by ▴ 180
0
votes
2
replies
527
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 5 months ago by • 0
0
votes
1
reply
745
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 4 months ago by ▴ 60 • written 4 months ago by • 0
4
votes
2
replies
672
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Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 6 months ago by ▴ 180
2
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3
replies
1.5k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 8 months ago by 16k • written 8 months ago by • 0
3
votes
4
replies
652
views
Store output of matchPWM()
biostrings Biostrings
9 months ago • updated 8 months ago mat149 ▴ 80
0
votes
1
reply
446
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 10 months ago by 67k • written 10 months ago by • 0
2
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2
replies
1.3k
views
From a DNAStringSet to a data.frame
Biostrings
10 months ago ramiro.barrantes ▴ 10
1
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5
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871
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
10 months ago Gerhard Thallinger ▴ 180
0
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0
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359
views
How to search for a string in a DNAStringSet dataset?
Biostrings
12 months ago Angela Michalichyn • 0
2
votes
6
replies
1.2k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 16 months ago by 16k • written 16 months ago by • 0
1
vote
3
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917
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AAbin vs DNAbin structures
Biostrings
updated 16 months ago by 67k • written 17 months ago by • 0
0
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2
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1.0k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 21 months ago by ▴ 70
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0
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586
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
23 months ago Gilles • 0
0
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0
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741
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.0 years ago Mario Dejung • 0
0
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0
replies
893
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.1 years ago vonSkopnik • 0
0
votes
2
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1.0k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 3 months ago by ▴ 20 • written 2.1 years ago by • 0
0
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0
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864
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.2 years ago biong • 0
0
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8
replies
1.7k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.3 years ago Brett • 0
3
votes
5
replies
1.9k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.3 years ago by 16k • written 2.3 years ago by • 0
2
votes
2
replies
2.6k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.3 years ago Mog • 0
0
votes
1
reply
992
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.4 years ago by 16k • written 2.8 years ago by • 0
0
votes
2
replies
2.0k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.7 years ago by 16k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.4k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
1
vote
0
replies
1.3k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.9 years ago L ▴ 50
0
votes
4
replies
2.5k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
0
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0
replies
881
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.9 years ago vonSkopnik • 0
5
votes
5
replies
1.9k
views
Changing genetic_code_table in Biostrings
Biostrings
2.9 years ago Sam • 0
0
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0
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652
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.9 years ago Charles Plessy ▴ 180
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0
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846
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.0 years ago Charles Plessy ▴ 180
0
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2
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1.0k
views
Simple subject extraction question with biostrings
Biostrings
3.0 years ago James • 0
1
vote
6
replies
2.0k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 180
1
vote
2
replies
1.6k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.2 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.2k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
1
vote
2
replies
1.3k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.2 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.9k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.4 years ago HELEN • 0
0
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0
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1.0k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.5 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.1k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.6 years ago by 16k • written 3.7 years ago by ▴ 260
0
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0
replies
1.2k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.8 years ago adklts • 0
0
votes
3
replies
1.2k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.9 years ago • updated 3.8 years ago sieminsk • 0
3
votes
2
replies
2.4k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.0 years ago Benjamin ▴ 20
2
votes
3
replies
1.3k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.1 years ago Nicholas Cooley • 0
6
votes
5
replies
2.2k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.2 years ago Bogdan ▴ 670
1
vote
1
reply
1.0k
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.3 years ago by ▴ 10 • written 4.3 years ago by • 0
0
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0
replies
875
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.4 years ago JennyS • 0
0
votes
3
replies
2.0k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
50 results • Page 1 of 1
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
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Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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