Showing : BioStrings • reset
1
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3
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112
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readDNAStringSet with non DNA characters
Biostrings
3 days ago • updated 2 days ago biomiha ▴ 20
0
votes
2
replies
164
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Create consensusMatrix for codon bases
Biostrings
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
1
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7
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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 7 months ago by ★ 3.4k • written 9 months ago by ▴ 20
0
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1
reply
314
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Matching patterns in an AAStringset
Biostrings
updated 9 months ago by ▴ 70 • written 9 months ago by • 0
1
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4
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945
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 10 months ago by • 0
1
vote
3
replies
870
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
updated 5 months ago by • 0 • written 11 months ago by • 0
1
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2
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712
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
715
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 12 months ago by • 0
0
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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
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2
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939
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Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 14 months ago by ▴ 180
2
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3
replies
1.7k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 15 months ago by 16k • written 15 months ago by • 0
3
votes
4
replies
864
views
Store output of matchPWM()
biostrings Biostrings
16 months ago mat149 ▴ 80
0
votes
1
reply
640
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
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2
replies
2.1k
views
From a DNAStringSet to a data.frame
Biostrings
18 months ago ramiro.barrantes ▴ 10
1
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5
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1.2k
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
18 months ago Gerhard Thallinger ▴ 180
0
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0
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467
views
How to search for a string in a DNAStringSet dataset?
Biostrings
20 months ago Angela Michalichyn • 0
2
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6
replies
1.4k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 23 months ago by 16k • written 23 months ago by • 0
1
vote
3
replies
1.2k
views
AAbin vs DNAbin structures
Biostrings
updated 2.0 years ago by 68k • written 2.0 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
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0
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737
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.6 years ago Gilles • 0
0
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0
replies
912
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.7 years ago Mario Dejung • 0
0
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0
replies
1.1k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.7 years ago vonSkopnik • 0
0
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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
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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
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8
replies
2.1k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.9 years ago Brett • 0
3
votes
5
replies
2.2k
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 3.4 years ago by • 0
0
votes
2
replies
2.3k
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 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
1
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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
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4
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2.9k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
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0
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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
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0
replies
772
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
3.6 years ago Charles Plessy ▴ 180
0
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0
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1.0k
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.6 years ago Charles Plessy ▴ 180
0
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2
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1.3k
views
Simple subject extraction question with biostrings
Biostrings
3.6 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
3.8 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.7k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.8 years ago by 16k • written 3.8 years ago by • 0
1
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2
replies
1.5k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.8 years ago Madza Farias-Virgens • 0
0
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4
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4.4k
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
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0
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1.1k
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
4.1 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 4.3 years ago by ▴ 270
0
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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
1.4k
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 4.9 years ago by ▴ 10 • written 4.9 years ago by • 0
292 results • Page 1 of 6
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Comment: Visualization of Functional Enrichment Result with enrichplot: How to control la by zhaoqiansun0592 • 0
Wow, this is super helpful! I always struggle with label sizes in enrichplot. Glad to see a solution using gginnards([Pasjans][1]) and ggre…
Comment: Could we detect difference at pathway level but not significant different at gen by zhaoqiansun0592 • 0
Interesting question! It's cool that ChatGPT4 gave such a helpful answer. I've also been wondering if pathways([space waves][1]) can show d…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by zhaoqiansun0592 • 0
Good to know there are workarounds for these tricky [doodle baseball][1]! Thanks for sharing the tips! [1]: https://doodle-baseball.cc/
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
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Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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