Showing : biostrings • reset
0
votes
3
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443
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Create consensusMatrix for codon bases
Biostrings
updated 9 weeks ago by ★ 4.0k • written 5 months ago by • 0
1
vote
3
replies
475
views
readDNAStringSet with non DNA characters
Biostrings
4 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
3.2k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 12 months ago by ★ 3.4k • written 13 months ago by ▴ 20
0
votes
1
reply
465
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 15 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
844
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 13 months ago by ▴ 70 • written 15 months ago by ▴ 180
0
votes
2
replies
848
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 17 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
1.2k
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 20 months ago by 16k • written 20 months ago by • 0
3
votes
4
replies
1.0k
views
Store output of matchPWM()
biostrings Biostrings
21 months ago • updated 20 months ago mat149 ▴ 80
0
votes
1
reply
739
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 22 months ago by 68k • written 22 months ago by • 0
2
votes
2
replies
2.5k
views
From a DNAStringSet to a data.frame
Biostrings
22 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
560
views
How to search for a string in a DNAStringSet dataset?
Biostrings
2.0 years 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
821
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
3.0 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
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0
replies
1.2k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
3.1 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
3.3 years ago • updated 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
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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
1.8k
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
3.9 years ago L ▴ 50
0
votes
4
replies
3.1k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.9 years ago by 68k • written 3.9 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
856
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
4.0 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
4.1k
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
1.7k
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
4.5 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.8k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 4.6 years ago by 16k • written 4.7 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
3.0k
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
3.1k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
5.2 years ago Bogdan ▴ 670
1
vote
1
reply
1.3k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by • 0
292 results • Page 1 of 6
Recent ...
Replies
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. Your use…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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