Showing : Biostrings • reset
4
votes
8
replies
739
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 4 days ago by ★ 3.4k • written 7 days ago by ▴ 20
0
votes
1
reply
129
views
Matching patterns in an AAStringset
Biostrings
updated 14 days ago by ▴ 60 • written 14 days ago by • 0
1
vote
4
replies
643
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 8 weeks ago by • 0
1
vote
3
replies
331
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 10 weeks ago by • 0
1
vote
2
replies
431
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 4 days ago by ▴ 60 • written 10 weeks ago by ▴ 180
0
votes
2
replies
496
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 4 months ago by • 0
0
votes
1
reply
633
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 3 months ago by ▴ 60 • written 3 months ago by • 0
4
votes
2
replies
619
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 5 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 6 months ago by 16k • written 7 months ago by • 0
3
votes
4
replies
604
views
Store output of matchPWM()
biostrings Biostrings
7 months ago mat149 ▴ 80
0
votes
1
reply
413
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 9 months ago by 67k • written 9 months ago by • 0
2
votes
2
replies
1.1k
views
From a DNAStringSet to a data.frame
Biostrings
9 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
826
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
9 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
343
views
How to search for a string in a DNAStringSet dataset?
Biostrings
11 months ago Angela Michalichyn • 0
2
votes
6
replies
1.2k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 14 months ago by 16k • written 15 months ago by • 0
1
vote
3
replies
881
views
AAbin vs DNAbin structures
Biostrings
updated 15 months ago by 67k • written 15 months ago by • 0
0
votes
2
replies
993
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 20 months ago by ▴ 70
0
votes
0
replies
564
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
22 months ago Gilles • 0
0
votes
0
replies
713
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
23 months ago Mario Dejung • 0
0
votes
0
replies
869
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
24 months ago vonSkopnik • 0
0
votes
2
replies
988
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 10 weeks ago by ▴ 20 • written 2.0 years ago by • 0
0
votes
0
replies
833
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.1 years ago biong • 0
0
votes
8
replies
1.6k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.2 years ago Brett • 0
3
votes
5
replies
1.8k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
2
votes
2
replies
2.6k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.2 years ago Mog • 0
0
votes
1
reply
968
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.4 years ago by 16k • written 2.7 years ago by • 0
0
votes
2
replies
1.9k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.6 years ago by 16k • written 2.6 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 2.7 years ago by ▴ 780 • written 2.7 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
2.8 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 2.8 years ago by 67k • written 2.8 years ago by • 0
0
votes
0
replies
863
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.8 years ago vonSkopnik • 0
5
votes
5
replies
1.9k
views
Changing genetic_code_table in Biostrings
Biostrings
2.9 years ago • updated 2.8 years ago Sam • 0
0
votes
0
replies
630
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.9 years ago Charles Plessy ▴ 180
0
votes
0
replies
825
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.9 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.0k
views
Simple subject extraction question with biostrings
Biostrings
2.9 years ago James • 0
1
vote
6
replies
2.0k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 3.0 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
3.1 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.2k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
1
vote
2
replies
1.3k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.1 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.8k
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
977
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.4 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.1k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.5 years ago by 16k • written 3.6 years ago by ▴ 260
0
votes
0
replies
1.1k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.7 years ago adklts • 0
0
votes
3
replies
1.2k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.8 years ago • updated 3.7 years ago sieminsk • 0
3
votes
2
replies
2.4k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.9 years ago Benjamin ▴ 20
2
votes
3
replies
1.3k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.0 years ago Nicholas Cooley • 0
6
votes
5
replies
2.1k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.1 years ago Bogdan ▴ 670
1
vote
1
reply
979
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by • 0
0
votes
0
replies
853
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.3 years ago JennyS • 0
0
votes
3
replies
2.0k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by freemanmclaughlin9969289 • 0
Tools such as Pathway Analysis with Deweighting of Overlapping Genes ([block blast][1]) or Gene Set Enrichment Analysis for Single Cell RNA…
Comment: How to get around the warning message: mzR has been built against a different Rc by Nan • 0
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your a…
Answer: EuroBioC2023 abstract submission closing soon! by excess.gecko.shso • 0
Don't miss out! EuroBioC2023 abstract submissions are nearing the deadline. Sharpen your scientific [Wordle Game][1] skills and submit your…
Answer: EuroBioC2024 abstract submission is open! by excess.gecko.shso • 0
EuroBioC2024 abstract submissions are now open! Join the Oxford conference from Sep 4-6. Submit your abstract by April 26 for short talks, …
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
Awards • All
Popular Question to bpshtiwan ▴ 10
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Locations • All
., 35 minutes ago
United Kingdom, 2 hours ago
us, 2 hours ago
UPF, Barcelona, Spain, 3 hours ago
India, 4 hours ago
Traffic: 507 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