Showing : BioStrings • reset
0
votes
3
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425
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Create consensusMatrix for codon bases
Biostrings
updated 7 weeks ago by ★ 4.0k • written 5 months ago by • 0
1
vote
3
replies
464
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readDNAStringSet with non DNA characters
Biostrings
4 months ago • updated 3 months ago biomiha ▴ 20
1
vote
7
replies
2.7k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 9 months ago by • 0 • written 4.1 years ago by ▴ 180
4
votes
9
replies
3.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 11 months ago by ★ 3.4k • written 13 months ago by ▴ 20
0
votes
1
reply
433
views
Matching patterns in an AAStringset
Biostrings
updated 13 months ago by ▴ 70 • written 13 months ago by • 0
1
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4
replies
1.1k
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 14 months ago by • 0
1
vote
4
replies
1.2k
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 15 months ago by • 0
1
vote
2
replies
826
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 12 months ago by ▴ 70 • written 15 months ago by ▴ 180
0
votes
2
replies
831
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 16 months ago by • 0
0
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1
reply
1.5k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 16 months ago by ▴ 70 • written 16 months ago by • 0
4
votes
2
replies
1.1k
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 18 months ago by ▴ 180
2
votes
3
replies
1.9k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 19 months ago by 16k • written 19 months ago by • 0
3
votes
4
replies
997
views
Store output of matchPWM()
biostrings Biostrings
20 months ago mat149 ▴ 80
0
votes
1
reply
727
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 21 months ago by 68k • written 21 months ago by • 0
2
votes
2
replies
2.4k
views
From a DNAStringSet to a data.frame
Biostrings
21 months ago ramiro.barrantes ▴ 10
1
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5
replies
1.4k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
22 months ago Gerhard Thallinger ▴ 180
0
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0
replies
554
views
How to search for a string in a DNAStringSet dataset?
Biostrings
24 months ago Angela Michalichyn • 0
2
votes
6
replies
1.6k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.3 years ago by 16k • written 2.3 years ago by • 0
1
vote
3
replies
1.4k
views
AAbin vs DNAbin structures
Biostrings
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
2
replies
1.4k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.7 years ago by ▴ 70
0
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0
replies
810
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.9 years ago Gilles • 0
0
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0
replies
1.0k
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
3.0 years ago Mario Dejung • 0
0
votes
0
replies
1.2k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
3.0 years ago vonSkopnik • 0
0
votes
2
replies
1.4k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 15 months ago by ▴ 20 • written 3.1 years ago by • 0
0
votes
0
replies
1.2k
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
3.2 years ago biong • 0
0
votes
8
replies
2.3k
views
translate errors in fastq file reading
translate biostrings Biostrings
3.2 years ago Brett • 0
3
votes
5
replies
2.4k
views
Biostrings multiple pattern match
pattern Biostrings
updated 3.3 years ago by 16k • written 3.3 years ago by • 0
2
votes
2
replies
3.5k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.3 years ago Mog • 0
0
votes
1
reply
1.4k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 3.4 years ago by 16k • written 3.8 years ago by • 0
0
votes
2
replies
2.5k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.7 years ago by 16k • written 3.7 years ago by ▴ 10
0
votes
1
reply
1.7k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
1
vote
0
replies
1.6k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.8 years ago L ▴ 50
0
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4
replies
3.0k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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0
replies
1.1k
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.9 years ago vonSkopnik • 0
5
votes
5
replies
2.5k
views
Changing genetic_code_table in Biostrings
Biostrings
3.9 years ago Sam • 0
0
votes
0
replies
845
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.9 years ago Charles Plessy ▴ 180
0
votes
0
replies
1.1k
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.9 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.4k
views
Simple subject extraction question with biostrings
Biostrings
4.0 years ago James • 0
1
vote
2
replies
2.1k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
votes
3
replies
4.0k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.7k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
4.4 years ago HELEN • 0
0
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0
replies
1.2k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
4.4 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 4.6 years ago by 16k • written 4.6 years ago by ▴ 270
0
votes
0
replies
1.4k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.8 years ago adklts • 0
0
votes
3
replies
1.6k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.8 years ago sieminsk • 0
3
votes
2
replies
2.9k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
5.0 years ago Benjamin ▴ 20
2
votes
3
replies
1.7k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
5.1 years ago Nicholas Cooley • 0
6
votes
5
replies
3.0k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
5.1 years ago Bogdan ▴ 670
1
vote
1
reply
1.3k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.2 years ago by ▴ 10 • written 5.3 years ago by • 0
292 results • Page 1 of 6
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Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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