Showing : BioStrings • reset
1
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4
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592
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Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 24 days ago by • 0
1
vote
3
replies
267
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 5 weeks ago by • 0
1
vote
1
reply
296
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
5 weeks ago Gerhard Thallinger ▴ 180
0
votes
2
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472
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
492
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 8 weeks ago by ▴ 60 • written 9 weeks ago by • 0
4
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2
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573
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 4 months ago by ▴ 180
2
votes
3
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1.4k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 5 months ago by 16k • written 5 months ago by • 0
3
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4
replies
567
views
Store output of matchPWM()
biostrings Biostrings
6 months ago mat149 ▴ 80
0
votes
1
reply
378
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 7 months ago by 67k • written 7 months ago by • 0
2
votes
2
replies
964
views
From a DNAStringSet to a data.frame
Biostrings
7 months ago ramiro.barrantes ▴ 10
1
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5
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773
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
322
views
How to search for a string in a DNAStringSet dataset?
Biostrings
10 months ago Angela Michalichyn • 0
2
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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
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3
replies
840
views
AAbin vs DNAbin structures
Biostrings
updated 14 months ago by 67k • written 14 months ago by • 0
0
votes
2
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958
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 18 months ago by ▴ 70
0
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0
replies
541
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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682
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
22 months ago Mario Dejung • 0
0
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0
replies
844
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
23 months ago vonSkopnik • 0
0
votes
2
replies
951
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
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800
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
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8
replies
1.6k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.1 years ago Brett • 0
3
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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
2.1 years ago Mog • 0
0
votes
1
reply
941
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
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0
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829
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.7 years ago vonSkopnik • 0
5
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5
replies
1.8k
views
Changing genetic_code_table in Biostrings
Biostrings
2.8 years ago Sam • 0
0
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0
replies
604
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.8 years ago Charles Plessy ▴ 180
0
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0
replies
808
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.8 years ago Charles Plessy ▴ 180
0
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2
replies
979
views
Simple subject extraction question with biostrings
Biostrings
2.8 years ago James • 0
1
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6
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2.0k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.9 years ago by 16k • written 2.9 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
3.2 years ago HELEN • 0
0
votes
0
replies
951
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 3.4 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
3.8 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
953
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
831
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.2 years ago jennyl.smith12 • 0
0
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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
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Answer: Allele frequencies for ALL alleles of one SNP ? by Abiologist • 0
I've discovered that rsnps::ncbi_snp_query(snp_id) does actually give this information - at the bottom of the result$maf_population table. …
Answer: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k
Hi, if you want to do some formal inference about the effect of a drug at RNA level, then I would recommend you doing a differential expres…
Answer: How to get The evolutionary conservation scores for lncRNAs by the phastCons100w by Robert Castelo ★ 3.4k
The `phastCons100way.UCSC.hg38` annotation package, storing conservation scores of the human genome version `hg38`, should be queried with …
Comment: Package needs internet access by firestar ▴ 20
That worked! Thanks! I created the genome file locally and uploaded that. I didn't really think that BSgenome.Hsapiens.UCSC.hg38 was only u…
Comment: limma technical repeat correction by john • 0
Hi @gordonsmyth, Thank you very much for your response. The normalization process involves multiple steps and they provide a normalised f…
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Answer: Package needs internet access
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Comment: Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
Dotplot from enricher outputting very few genes
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