Showing : biostrings • reset
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Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated just now by ★ 4.2k • written 2 days ago by • 0
3
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4
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314
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Store output of matchPWM()
biostrings Biostrings
28 days ago • updated 16 days ago mat149 ▴ 70
0
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1
reply
168
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 9 weeks ago by 66k • written 9 weeks ago by • 0
2
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2
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285
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From a DNAStringSet to a data.frame
Biostrings
9 weeks ago ramiro.barrantes ▴ 10
1
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5
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473
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
11 weeks ago • updated 10 weeks ago Gerhard Thallinger ▴ 180
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0
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179
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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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809
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 8 months ago by • 0
1
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3
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561
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AAbin vs DNAbin structures
Biostrings
updated 8 months ago by 66k • written 8 months ago by • 0
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2
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728
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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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383
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Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
15 months ago Gilles • 0
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0
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498
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
16 months ago Mario Dejung • 0
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0
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637
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
17 months ago vonSkopnik • 0
0
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1
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694
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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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619
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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
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8
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1.2k
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translate errors in fastq file reading
translate biostrings Biostrings
19 months ago Brett • 0
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5
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1.5k
views
Biostrings multiple pattern match
pattern Biostrings
updated 20 months ago by 16k • written 20 months ago by • 0
2
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2
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1.9k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
20 months ago Mog • 0
0
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1
reply
754
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
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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
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1
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999
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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
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0
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1.0k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.2 years ago L ▴ 50
0
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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
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697
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How to make a pairwiseAlignment of circular sequences
Biostrings
2.3 years ago vonSkopnik • 0
5
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5
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1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.3 years ago Sam • 0
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0
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485
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.3 years ago Charles Plessy ▴ 180
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0
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672
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.3 years ago Charles Plessy ▴ 180
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2
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789
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Simple subject extraction question with biostrings
Biostrings
2.3 years ago James • 0
1
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6
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1.7k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.4 years ago by 16k • written 2.5 years ago by ▴ 180
1
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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
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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
1.1k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
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4
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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
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0
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783
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Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.8 years ago emmanuel.verde2939 • 0
4
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9
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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
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0
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954
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.2 years ago adklts • 0
0
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3
replies
988
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
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3
replies
1.0k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.5 years ago Nicholas Cooley • 0
6
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5
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1.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.5 years ago Bogdan ▴ 670
1
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1
reply
797
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
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694
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.7 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 4.0 years ago by 66k • written 4.0 years ago by • 0
0
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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
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1
reply
872
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
994
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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604
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Detect unique deletions in DNAMultipleAlignment
biostrings
4.1 years ago multipleseqs • 0
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2
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997
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.2 years ago mb2subi • 0
1
vote
2
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820
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
50 results • Page 1 of 1
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Replies
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
The source script of the C function is available, just take it and compile the longestConsecutive function yourself, that's the easiest I g…
Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process") by James W. MacDonald 66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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