Showing : biostrings • reset
4
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9
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2.3k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 10 weeks ago by ★ 3.4k • written 3 months ago by ▴ 20
0
votes
1
reply
211
views
Matching patterns in an AAStringset
Biostrings
updated 3 months ago by ▴ 60 • written 3 months ago by • 0
1
vote
4
replies
805
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 5 months ago by • 0
1
vote
3
replies
620
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
updated 14 days ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
555
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 3 months ago by ▴ 60 • written 5 months ago by ▴ 180
0
votes
2
replies
587
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 7 months ago by • 0
0
votes
1
reply
968
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 6 months ago by ▴ 60 • written 6 months ago by • 0
4
votes
2
replies
775
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 8 months ago by ▴ 180
2
votes
3
replies
1.5k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 10 months ago by 16k • written 10 months ago by • 0
3
votes
4
replies
738
views
Store output of matchPWM()
biostrings Biostrings
11 months ago • updated 10 months ago mat149 ▴ 80
0
votes
1
reply
513
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 12 months ago by 68k • written 12 months ago by • 0
2
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2
replies
1.7k
views
From a DNAStringSet to a data.frame
Biostrings
12 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
972
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
13 months ago • updated 12 months ago Gerhard Thallinger ▴ 180
0
votes
0
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398
views
How to search for a string in a DNAStringSet dataset?
Biostrings
14 months ago Angela Michalichyn • 0
2
votes
6
replies
1.3k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 18 months ago by 16k • written 18 months ago by • 0
1
vote
3
replies
1.0k
views
AAbin vs DNAbin structures
Biostrings
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
replies
1.1k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 23 months ago by ▴ 70
0
votes
0
replies
636
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.1 years ago Gilles • 0
0
votes
0
replies
791
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.2 years ago Mario Dejung • 0
0
votes
0
replies
951
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.3 years ago vonSkopnik • 0
0
votes
2
replies
1.1k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 5 months ago by ▴ 20 • written 2.3 years ago by • 0
0
votes
0
replies
927
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.4 years ago biong • 0
0
votes
8
replies
1.9k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.4 years ago Brett • 0
3
votes
5
replies
2.0k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
2
votes
2
replies
2.9k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.5 years ago Mog • 0
0
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1
reply
1.1k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.6 years ago by 16k • written 3.0 years ago by • 0
0
votes
2
replies
2.1k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 10
0
votes
1
reply
1.5k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
1
vote
0
replies
1.3k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.1 years ago L ▴ 50
0
votes
4
replies
2.7k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
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0
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931
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.1 years ago vonSkopnik • 0
5
votes
5
replies
2.1k
views
Changing genetic_code_table in Biostrings
Biostrings
3.1 years ago Sam • 0
0
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0
replies
691
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.1 years ago Charles Plessy ▴ 180
0
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0
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890
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.2 years ago Charles Plessy ▴ 180
0
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2
replies
1.1k
views
Simple subject extraction question with biostrings
Biostrings
3.2 years ago James • 0
1
vote
6
replies
2.2k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 180
1
vote
2
replies
1.7k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.4 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.4k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.4 years ago by 16k • written 3.4 years ago by • 0
1
vote
2
replies
1.4k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.4 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.1k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.6 years ago HELEN • 0
0
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0
replies
1.1k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.7 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.3k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.8 years ago by 16k • written 3.9 years ago by ▴ 260
0
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0
replies
1.2k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.0 years ago adklts • 0
0
votes
3
replies
1.3k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.0 years ago sieminsk • 0
3
votes
2
replies
2.6k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.2 years ago Benjamin ▴ 20
2
votes
3
replies
1.4k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.3 years ago Nicholas Cooley • 0
6
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5
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2.4k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.4 years ago • updated 4.3 years ago Bogdan ▴ 670
1
vote
1
reply
1.1k
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.5 years ago by ▴ 10 • written 4.5 years ago by • 0
0
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0
replies
927
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.5 years ago JennyS • 0
0
votes
3
replies
2.1k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
50 results • Page 1 of 1
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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.8k
That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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