Showing : Biostrings • reset
4
votes
8
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1.5k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 16 days ago by ★ 3.4k • written 19 days ago by ▴ 20
0
votes
1
reply
145
views
Matching patterns in an AAStringset
Biostrings
updated 27 days ago by ▴ 60 • written 27 days ago by • 0
1
vote
4
replies
664
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 10 weeks ago by • 0
1
vote
3
replies
349
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 12 weeks ago by • 0
1
vote
2
replies
451
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 17 days ago by ▴ 60 • written 12 weeks ago by ▴ 180
0
votes
2
replies
505
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 4 months ago by • 0
0
votes
1
reply
658
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 3 months ago by ▴ 60 • written 3 months ago by • 0
4
votes
2
replies
636
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 5 months ago by ▴ 180
2
votes
3
replies
1.4k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 7 months ago by 16k • written 7 months ago by • 0
3
votes
4
replies
622
views
Store output of matchPWM()
biostrings Biostrings
8 months ago • updated 7 months ago mat149 ▴ 80
0
votes
1
reply
425
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 9 months ago by 67k • written 9 months ago by • 0
2
votes
2
replies
1.2k
views
From a DNAStringSet to a data.frame
Biostrings
9 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
844
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
10 months ago • updated 9 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
349
views
How to search for a string in a DNAStringSet dataset?
Biostrings
11 months ago Angela Michalichyn • 0
2
votes
6
replies
1.2k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 15 months ago by 16k • written 15 months ago by • 0
1
vote
3
replies
889
views
AAbin vs DNAbin structures
Biostrings
updated 16 months ago by 67k • written 16 months ago by • 0
0
votes
2
replies
1.0k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 20 months ago by ▴ 70
0
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0
replies
574
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
23 months ago Gilles • 0
0
votes
0
replies
722
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
24 months ago Mario Dejung • 0
0
votes
0
replies
873
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.0 years ago vonSkopnik • 0
0
votes
2
replies
1000
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 12 weeks ago by ▴ 20 • written 2.1 years ago by • 0
0
votes
0
replies
838
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
votes
8
replies
1.7k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.2 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
979
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.4 years ago by 16k • written 2.7 years ago by • 0
0
votes
2
replies
1.9k
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
1.3k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
1
vote
0
replies
1.2k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.8 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 2.8 years ago by 67k • written 2.8 years ago by • 0
0
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0
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868
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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637
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.9 years ago Charles Plessy ▴ 180
0
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0
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830
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.9 years ago Charles Plessy ▴ 180
0
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2
replies
1.0k
views
Simple subject extraction question with biostrings
Biostrings
2.9 years ago James • 0
1
vote
6
replies
2.0k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 3.0 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
3.1 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.2k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
1
vote
2
replies
1.3k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.1 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.8k
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
votes
0
replies
981
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.4 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 3.6 years ago by ▴ 260
0
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0
replies
1.1k
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
3.8 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
2.1k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.1 years ago Bogdan ▴ 670
1
vote
1
reply
990
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by • 0
0
votes
0
replies
861
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.3 years ago JennyS • 0
0
votes
3
replies
2.0k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
50 results • Page 1 of 1
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Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
So I changed it to ~0 + group (with the same plot), but I still don't know if it's good or what to fix if not.
Answer: Newbie Question - adding metadata to an analysis by James W. MacDonald 67k
See [Section 4][1]. But do note that you do not need for the `phenoData` slot to contain the data. You can simply have a 'targets' data.fra…
Comment: Want numbers in DESeq to be seen as numerical, not categorical by swbarnes2 ★ 1.4k
How did you import the data? Did you accidently leave in `stringAsFactors=True`? But I'm not entirely sure that you don't want that to be…
Comment: MissMethyl failed to use gometh function for EPICv2 by James W. MacDonald 67k
By version 1.38.0, I mean version 1.38.0 of `MissMethyl`.
Answer: MissMethyl failed to use gometh function for EPICv2 by James W. MacDonald 67k
You need to [upgrade to the release version of Bioconductor][1]. You have version 1.38.0 installed which indicates that you are using the p…
Votes
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: Theoretical WGCNA Question
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
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