Showing : Biostrings • reset
1
vote
4
replies
599
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 29 days ago by • 0
1
vote
3
replies
273
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 5 weeks ago by • 0
1
vote
1
reply
302
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
5 weeks ago Gerhard Thallinger ▴ 180
0
votes
2
replies
474
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 12 weeks ago by • 0
0
votes
1
reply
507
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 9 weeks ago by ▴ 60 • written 10 weeks ago by • 0
4
votes
2
replies
578
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 4 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 5 months ago by 16k • written 6 months ago by • 0
3
votes
4
replies
572
views
Store output of matchPWM()
biostrings Biostrings
6 months ago mat149 ▴ 80
0
votes
1
reply
385
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 8 months ago by 67k • written 8 months ago by • 0
2
votes
2
replies
979
views
From a DNAStringSet to a data.frame
Biostrings
8 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
783
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
326
views
How to search for a string in a DNAStringSet dataset?
Biostrings
10 months ago Angela Michalichyn • 0
2
votes
6
replies
1.1k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 13 months ago by 16k • written 13 months ago by • 0
1
vote
3
replies
843
views
AAbin vs DNAbin structures
Biostrings
updated 14 months ago by 67k • written 14 months ago by • 0
0
votes
2
replies
963
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 19 months ago by ▴ 70
0
votes
0
replies
547
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
21 months ago Gilles • 0
0
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0
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686
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
22 months ago Mario Dejung • 0
0
votes
0
replies
847
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
23 months ago vonSkopnik • 0
0
votes
2
replies
959
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 5 weeks ago by ▴ 20 • written 23 months ago by • 0
0
votes
0
replies
808
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.0 years ago biong • 0
0
votes
8
replies
1.6k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.1 years ago Brett • 0
3
votes
5
replies
1.8k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
2
votes
2
replies
2.5k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.2 years ago • updated 2.1 years ago Mog • 0
0
votes
1
reply
944
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.3 years ago by 16k • written 2.6 years ago by • 0
0
votes
2
replies
1.8k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.5 years ago by 16k • written 2.5 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 2.6 years ago by ▴ 780 • written 2.6 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
2.7 years ago L ▴ 50
0
votes
4
replies
2.4k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
0
votes
0
replies
832
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.8 years ago vonSkopnik • 0
5
votes
5
replies
1.8k
views
Changing genetic_code_table in Biostrings
Biostrings
2.8 years ago Sam • 0
0
votes
0
replies
608
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.8 years ago Charles Plessy ▴ 180
0
votes
0
replies
809
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.8 years ago Charles Plessy ▴ 180
0
votes
2
replies
984
views
Simple subject extraction question with biostrings
Biostrings
2.8 years ago James • 0
1
vote
6
replies
2.0k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.9 years ago by 16k • written 3.0 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
3.0 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.1k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
1
vote
2
replies
1.2k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.0 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.7k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.3 years ago HELEN • 0
0
votes
0
replies
954
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.3 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.0k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.5 years ago by 16k • written 3.5 years ago by ▴ 260
0
votes
0
replies
1.1k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.6 years ago adklts • 0
0
votes
3
replies
1.2k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.7 years ago • updated 3.6 years ago sieminsk • 0
3
votes
2
replies
2.3k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.9 years ago • updated 3.8 years ago Benjamin ▴ 20
2
votes
3
replies
1.3k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.9 years ago Nicholas Cooley • 0
6
votes
5
replies
2.0k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.0 years ago Bogdan ▴ 670
1
vote
1
reply
957
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by • 0
0
votes
0
replies
833
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.2 years ago JennyS • 0
0
votes
3
replies
1.9k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
4
replies
2.7k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.5 years ago moldach ▴ 20
1
vote
1
reply
1.0k
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 90
50 results • Page 1 of 1
Recent ...
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Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
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Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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