Showing : Biostrings • reset
1
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7
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2.4k
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DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 6 weeks ago by • 0 • written 3.4 years ago by ▴ 180
4
votes
9
replies
2.4k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 3 months ago by ★ 3.4k • written 5 months ago by ▴ 20
0
votes
1
reply
246
views
Matching patterns in an AAStringset
Biostrings
updated 5 months ago by ▴ 60 • written 5 months ago by • 0
1
vote
4
replies
860
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 6 months ago by • 0
1
vote
3
replies
751
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
updated 8 weeks ago by • 0 • written 7 months ago by • 0
1
vote
2
replies
613
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 5 months ago by ▴ 60 • written 7 months ago by ▴ 180
0
votes
2
replies
637
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 8 months ago by • 0
0
votes
1
reply
1.0k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 8 months ago by ▴ 60 • written 8 months ago by • 0
4
votes
2
replies
832
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 10 months ago by ▴ 180
2
votes
3
replies
1.6k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 11 months ago by 16k • written 11 months ago by • 0
3
votes
4
replies
782
views
Store output of matchPWM()
biostrings Biostrings
12 months ago mat149 ▴ 80
0
votes
1
reply
556
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
2
replies
1.9k
views
From a DNAStringSet to a data.frame
Biostrings
14 months ago ramiro.barrantes ▴ 10
1
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5
replies
1.0k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
14 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
418
views
How to search for a string in a DNAStringSet dataset?
Biostrings
16 months ago Angela Michalichyn • 0
2
votes
6
replies
1.3k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 19 months ago by 16k • written 19 months ago by • 0
1
vote
3
replies
1.1k
views
AAbin vs DNAbin structures
Biostrings
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
2
replies
1.2k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.1 years ago by ▴ 70
0
votes
0
replies
680
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.3 years ago Gilles • 0
0
votes
0
replies
821
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.4 years ago Mario Dejung • 0
0
votes
0
replies
983
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.4 years ago vonSkopnik • 0
0
votes
2
replies
1.1k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 7 months ago by ▴ 20 • written 2.4 years ago by • 0
0
votes
0
replies
976
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.5 years ago biong • 0
0
votes
8
replies
1.9k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.6 years ago Brett • 0
3
votes
5
replies
2.1k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
2
votes
2
replies
3.0k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.6 years ago Mog • 0
0
votes
1
reply
1.1k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.8 years ago by 16k • written 3.1 years ago by • 0
0
votes
2
replies
2.2k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.5k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
1
vote
0
replies
1.4k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.2 years ago L ▴ 50
0
votes
4
replies
2.8k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
0
replies
967
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.2 years ago vonSkopnik • 0
5
votes
5
replies
2.2k
views
Changing genetic_code_table in Biostrings
Biostrings
3.3 years ago Sam • 0
0
votes
0
replies
724
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.3 years ago Charles Plessy ▴ 180
0
votes
0
replies
941
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.3 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.2k
views
Simple subject extraction question with biostrings
Biostrings
3.3 years ago James • 0
1
vote
2
replies
1.8k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.5 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
1
vote
2
replies
1.4k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.5 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.2k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.7 years ago HELEN • 0
0
votes
0
replies
1.1k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.8 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.4k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 270
0
votes
0
replies
1.3k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.1 years ago adklts • 0
0
votes
3
replies
1.4k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.2 years ago • updated 4.1 years ago sieminsk • 0
3
votes
2
replies
2.7k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.4 years ago • updated 4.3 years ago Benjamin ▴ 20
2
votes
3
replies
1.4k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.4 years ago Nicholas Cooley • 0
6
votes
5
replies
2.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.5 years ago Bogdan ▴ 670
1
vote
1
reply
1.1k
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
0
votes
0
replies
959
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.7 years ago JennyS • 0
0
votes
3
replies
2.2k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
50 results • Page 1 of 1
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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Votes
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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