Showing : biostrings • reset
3
votes
4
replies
307
views
Store output of matchPWM()
biostrings Biostrings
25 days ago • updated 12 days ago mat149 ▴ 70
0
votes
1
reply
161
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 8 weeks ago by 66k • written 8 weeks ago by • 0
2
votes
2
replies
271
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From a DNAStringSet to a data.frame
Biostrings
8 weeks ago ramiro.barrantes ▴ 10
1
vote
5
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471
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
11 weeks ago • updated 9 weeks ago Gerhard Thallinger ▴ 180
0
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0
replies
177
views
How to search for a string in a DNAStringSet dataset?
Biostrings
4 months ago Angela Michalichyn • 0
2
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6
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805
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
1
vote
3
replies
561
views
AAbin vs DNAbin structures
Biostrings
updated 8 months ago by 66k • written 8 months ago by • 0
0
votes
2
replies
726
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 13 months ago by ▴ 70
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0
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379
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
15 months ago Gilles • 0
0
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0
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496
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
16 months ago Mario Dejung • 0
0
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0
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635
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
17 months ago vonSkopnik • 0
0
votes
1
reply
690
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
17 months ago 潘晓光 • 0
0
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0
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615
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
18 months ago biong • 0
0
votes
8
replies
1.2k
views
translate errors in fastq file reading
translate biostrings Biostrings
19 months ago Brett • 0
3
votes
5
replies
1.5k
views
Biostrings multiple pattern match
pattern Biostrings
updated 20 months ago by 16k • written 20 months ago by • 0
2
votes
2
replies
1.9k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
20 months ago Mog • 0
0
votes
1
reply
753
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 21 months ago by 16k • written 2.1 years ago by • 0
0
votes
2
replies
1.3k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.0 years ago by 16k • written 2.0 years ago by ▴ 10
0
votes
1
reply
996
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
vote
0
replies
1.0k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.2 years ago L ▴ 50
0
votes
4
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1.9k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.2 years ago by 66k • written 2.2 years ago by • 0
0
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0
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695
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.3 years ago vonSkopnik • 0
5
votes
5
replies
1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.3 years ago Sam • 0
0
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0
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483
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.3 years ago Charles Plessy ▴ 180
0
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0
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671
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.3 years ago Charles Plessy ▴ 180
0
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2
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786
views
Simple subject extraction question with biostrings
Biostrings
2.3 years ago James • 0
1
vote
6
replies
1.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.4 years ago by 16k • written 2.5 years ago by ▴ 180
1
vote
2
replies
1.3k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
votes
3
replies
2.6k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
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2
replies
1.0k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
0
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4
replies
3.1k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.8 years ago HELEN • 0
0
votes
0
replies
781
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.8 years ago emmanuel.verde2939 • 0
4
votes
9
replies
1.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 250
0
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0
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946
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.2 years ago adklts • 0
0
votes
3
replies
983
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.2 years ago sieminsk • 0
3
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2
replies
1.8k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.4 years ago • updated 3.3 years ago Benjamin ▴ 20
2
votes
3
replies
1.0k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
6
votes
5
replies
1.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.5 years ago Bogdan ▴ 670
1
vote
1
reply
796
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.6 years ago by ▴ 10 • written 3.6 years ago by • 0
0
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0
replies
694
views
vcountPDict Out-of-Memory Errors
software error Biostrings
3.7 years ago jennyl.smith12 • 0
0
votes
3
replies
1.6k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.0 years ago by 66k • written 4.0 years ago by • 0
0
votes
4
replies
2.4k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.0 years ago moldach ▴ 20
1
vote
1
reply
866
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 90
0
votes
3
replies
1.4k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.1 years ago by ▴ 290 • written 4.1 years ago by ▴ 80
3
votes
1
reply
990
views
Biostrings matchPattern with lower case
biostrings
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 20
0
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0
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603
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.1 years ago multipleseqs • 0
0
votes
2
replies
994
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.2 years ago mb2subi • 0
1
vote
2
replies
816
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.3 years ago by ★ 4.2k • written 4.3 years ago by ▴ 50
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
2
votes
1
reply
735
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 4.4 years ago by 16k • written 4.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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