Showing : Biostrings • reset
1
vote
3
replies
253
views
readDNAStringSet with non DNA characters
Biostrings
17 days ago • updated 16 days ago biomiha ▴ 20
0
votes
2
replies
193
views
Create consensusMatrix for codon bases
Biostrings
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
1
vote
7
replies
2.5k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 5 months ago by • 0 • written 3.8 years ago by ▴ 180
4
votes
9
replies
2.7k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 8 months ago by ★ 3.4k • written 9 months ago by ▴ 20
0
votes
1
reply
324
views
Matching patterns in an AAStringset
Biostrings
updated 9 months ago by ▴ 70 • written 9 months ago by • 0
1
vote
4
replies
971
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 11 months ago by • 0
1
vote
3
replies
894
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
updated 6 months ago by • 0 • written 11 months ago by • 0
1
vote
2
replies
721
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 9 months ago by ▴ 70 • written 11 months ago by ▴ 180
0
votes
2
replies
728
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 13 months ago by • 0
0
votes
1
reply
1.2k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 12 months ago by ▴ 70 • written 12 months ago by • 0
4
votes
2
replies
959
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 14 months ago by ▴ 180
2
votes
3
replies
1.7k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 16 months ago by 16k • written 16 months ago by • 0
3
votes
4
replies
885
views
Store output of matchPWM()
biostrings Biostrings
17 months ago • updated 16 months ago mat149 ▴ 80
0
votes
1
reply
651
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 18 months ago by 68k • written 18 months ago by • 0
2
votes
2
replies
2.1k
views
From a DNAStringSet to a data.frame
Biostrings
18 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
1.2k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
19 months ago • updated 18 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
477
views
How to search for a string in a DNAStringSet dataset?
Biostrings
20 months ago Angela Michalichyn • 0
2
votes
6
replies
1.5k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
1
vote
3
replies
1.2k
views
AAbin vs DNAbin structures
Biostrings
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
2
replies
1.3k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.4 years ago by ▴ 70
0
votes
0
replies
746
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.6 years ago Gilles • 0
0
votes
0
replies
921
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.7 years ago Mario Dejung • 0
0
votes
0
replies
1.1k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.8 years ago vonSkopnik • 0
0
votes
2
replies
1.3k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 11 months ago by ▴ 20 • written 2.8 years ago by • 0
0
votes
0
replies
1.1k
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.9 years ago biong • 0
0
votes
8
replies
2.1k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.9 years ago Brett • 0
3
votes
5
replies
2.3k
views
Biostrings multiple pattern match
pattern Biostrings
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
2
votes
2
replies
3.2k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.0 years ago Mog • 0
0
votes
1
reply
1.2k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 3.1 years ago by 16k • written 3.5 years ago by • 0
0
votes
2
replies
2.4k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 10
0
votes
1
reply
1.6k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
1
vote
0
replies
1.5k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.5 years ago L ▴ 50
0
votes
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 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
0
replies
1.0k
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.6 years ago vonSkopnik • 0
5
votes
5
replies
2.4k
views
Changing genetic_code_table in Biostrings
Biostrings
3.6 years ago Sam • 0
0
votes
0
replies
777
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.6 years ago Charles Plessy ▴ 180
0
votes
0
replies
1.0k
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.7 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.3k
views
Simple subject extraction question with biostrings
Biostrings
3.7 years ago James • 0
1
vote
2
replies
1.9k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.9 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.8k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.9 years ago by 16k • written 3.9 years ago by • 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.9 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.5k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
4.1 years ago HELEN • 0
0
votes
0
replies
1.2k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
4.2 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.5k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 4.3 years ago by 16k • written 4.4 years ago by ▴ 270
0
votes
0
replies
1.3k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.5 years ago adklts • 0
0
votes
3
replies
1.5k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.5 years ago sieminsk • 0
3
votes
2
replies
2.8k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.7 years ago Benjamin ▴ 20
2
votes
3
replies
1.6k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.8 years ago Nicholas Cooley • 0
6
votes
5
replies
2.7k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.8 years ago Bogdan ▴ 670
1
vote
1
reply
1.2k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.0 years ago by ▴ 10 • written 5.0 years ago by • 0
292 results • Page 1 of 6
Recent ...
Replies
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Joseph • 0
Popular Question to Gordon Smyth 53k
Popular Question to zhe ▴ 20
Popular Question to Natalia • 0
Locations • All
United States, 30 minutes ago
Australia, 1 hour ago
Australia, 2 hours ago
Australia, 2 hours ago
USA, Los Angeles, USC, 4 hours ago
Traffic: 804 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6