Showing : biostrings • reset
0
votes
3
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313
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Create consensusMatrix for codon bases
Biostrings
updated 7 days ago by ★ 4.0k • written 3 months ago by • 0
1
vote
3
replies
401
views
readDNAStringSet with non DNA characters
Biostrings
10 weeks ago biomiha ▴ 20
1
vote
7
replies
2.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 7 months ago by • 0 • written 4.0 years ago by ▴ 180
4
votes
9
replies
2.9k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 10 months ago by ★ 3.4k • written 11 months ago by ▴ 20
0
votes
1
reply
369
views
Matching patterns in an AAStringset
Biostrings
updated 11 months ago by ▴ 70 • written 11 months ago by • 0
1
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4
replies
1.0k
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 13 months ago by • 0
1
vote
4
replies
1.0k
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 13 months ago by • 0
1
vote
2
replies
767
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
updated 11 months ago by ▴ 70 • written 13 months ago by ▴ 180
0
votes
2
replies
768
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 15 months ago by • 0
0
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1
reply
1.4k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
4
votes
2
replies
1.0k
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 16 months ago by ▴ 180
2
votes
3
replies
1.8k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 18 months ago by 16k • written 18 months ago by • 0
3
votes
4
replies
949
views
Store output of matchPWM()
biostrings Biostrings
19 months ago • updated 18 months ago mat149 ▴ 80
0
votes
1
reply
688
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 20 months ago by 68k • written 20 months ago by • 0
2
votes
2
replies
2.3k
views
From a DNAStringSet to a data.frame
Biostrings
20 months ago ramiro.barrantes ▴ 10
1
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5
replies
1.3k
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
21 months ago • updated 20 months ago Gerhard Thallinger ▴ 180
0
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0
replies
523
views
How to search for a string in a DNAStringSet dataset?
Biostrings
22 months ago Angela Michalichyn • 0
2
votes
6
replies
1.5k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
1
vote
3
replies
1.3k
views
AAbin vs DNAbin structures
Biostrings
updated 2.2 years ago by 68k • written 2.2 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 2.6 years ago by ▴ 70
0
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0
replies
773
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.8 years ago Gilles • 0
0
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0
replies
963
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.9 years ago Mario Dejung • 0
0
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0
replies
1.1k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.9 years ago vonSkopnik • 0
0
votes
2
replies
1.3k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 13 months ago by ▴ 20 • written 3.0 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
3.1 years ago biong • 0
0
votes
8
replies
2.2k
views
translate errors in fastq file reading
translate biostrings Biostrings
3.1 years ago Brett • 0
3
votes
5
replies
2.3k
views
Biostrings multiple pattern match
pattern Biostrings
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
2
votes
2
replies
3.3k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.2 years ago Mog • 0
0
votes
1
reply
1.3k
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 3.3 years ago by 16k • written 3.6 years ago by • 0
0
votes
2
replies
2.4k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3.6 years ago by 16k • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.7k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.6 years ago by ▴ 780 • written 3.6 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
3.7 years ago L ▴ 50
0
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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 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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0
replies
1.0k
views
How to make a pairwiseAlignment of circular sequences
Biostrings
3.8 years ago vonSkopnik • 0
5
votes
5
replies
2.4k
views
Changing genetic_code_table in Biostrings
Biostrings
3.8 years ago Sam • 0
0
votes
0
replies
813
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.8 years ago Charles Plessy ▴ 180
0
votes
0
replies
1.1k
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.8 years ago Charles Plessy ▴ 180
0
votes
2
replies
1.3k
views
Simple subject extraction question with biostrings
Biostrings
3.8 years ago James • 0
1
vote
2
replies
2.0k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.0 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.9k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.0 years ago Madza Farias-Virgens • 0
0
votes
4
replies
4.6k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
4.3 years ago HELEN • 0
0
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0
replies
1.2k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
4.3 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.6k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 270
0
votes
0
replies
1.4k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
4.7 years ago adklts • 0
0
votes
3
replies
1.5k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
4.7 years ago sieminsk • 0
3
votes
2
replies
2.9k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
4.9 years ago • updated 4.8 years ago Benjamin ▴ 20
2
votes
3
replies
1.7k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
5.0 years ago Nicholas Cooley • 0
6
votes
5
replies
2.8k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
5.0 years ago Bogdan ▴ 670
1
vote
1
reply
1.2k
views
Subset center regions of a set of different length sequences
Biostrings
updated 5.1 years ago by ▴ 10 • written 5.1 years ago by • 0
292 results • Page 1 of 6
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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