Showing : Biostrings • reset
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 23 days ago by 65k • written 23 days ago by • 0
2
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2
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190
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From a DNAStringSet to a data.frame
Biostrings
24 days ago ramiro.barrantes ▴ 10
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5
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403
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
6 weeks ago • updated 4 weeks ago Gerhard Thallinger ▴ 180
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0
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146
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How to search for a string in a DNAStringSet dataset?
Biostrings
3 months ago Angela Michalichyn • 0
2
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6
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746
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
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3
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488
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AAbin vs DNAbin structures
Biostrings
updated 7 months ago by 65k • written 7 months ago by • 0
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2
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673
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 11 months ago by ▴ 70
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345
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Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
14 months ago Gilles • 0
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0
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460
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
15 months ago Mario Dejung • 0
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0
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607
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
15 months ago vonSkopnik • 0
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1
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661
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Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
16 months ago 潘晓光 • 0
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0
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584
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
17 months ago biong • 0
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8
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1.1k
views
translate errors in fastq file reading
translate biostrings Biostrings
18 months ago • updated 17 months ago Brett • 0
3
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5
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1.4k
views
Biostrings multiple pattern match
pattern Biostrings
updated 18 months ago by 16k • written 18 months ago by • 0
2
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2
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1.7k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
18 months ago Mog • 0
0
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1
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720
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Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 20 months ago by 16k • written 2.0 years ago by • 0
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2
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1.2k
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Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 23 months ago by 16k • written 23 months ago by ▴ 10
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1
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949
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.0 years ago by ▴ 770 • written 2.0 years ago by • 0
1
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0
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949
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.1 years ago L ▴ 50
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4
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1.8k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
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0
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659
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How to make a pairwiseAlignment of circular sequences
Biostrings
2.2 years ago vonSkopnik • 0
5
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5
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1.4k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago Sam • 0
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0
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459
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.2 years ago Charles Plessy ▴ 180
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0
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639
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.2 years ago Charles Plessy ▴ 180
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2
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745
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Simple subject extraction question with biostrings
Biostrings
2.2 years ago James • 0
1
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6
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1.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.3 years ago by 16k • written 2.4 years ago by ▴ 180
1
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2
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1.2k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
2
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3
replies
2.4k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
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2
replies
996
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
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4
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3.0k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.7 years ago HELEN • 0
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0
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747
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.7 years ago emmanuel.verde2939 • 0
4
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9
replies
1.6k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 250
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0
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904
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
0
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3
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942
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.1 years ago • updated 3.0 years ago sieminsk • 0
3
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2
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1.7k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago • updated 3.2 years ago Benjamin ▴ 20
2
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3
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989
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Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.3 years ago Nicholas Cooley • 0
6
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5
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1.5k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago Bogdan ▴ 670
1
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1
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770
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.5 years ago by ▴ 10 • written 3.5 years ago by • 0
0
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0
replies
661
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.6 years ago jennyl.smith12 • 0
0
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3
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1.6k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
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4
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2.3k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
3.9 years ago moldach ▴ 20
1
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1
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838
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 90
0
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3
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1.3k
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Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.0 years ago by ▴ 290 • written 4.0 years ago by ▴ 80
3
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1
reply
941
views
Biostrings matchPattern with lower case
biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 20
0
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0
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581
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Detect unique deletions in DNAMultipleAlignment
biostrings
4.0 years ago multipleseqs • 0
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2
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965
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
1
vote
2
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785
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 50
5
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1
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3.0k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 4.3 years ago by ▴ 100 • written 4.3 years ago by ▴ 20
2
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1
reply
707
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 4.3 years ago by 16k • written 4.3 years ago by • 0
1
vote
1
reply
859
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 4.4 years ago by 25k • written 4.4 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) …
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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