Showing : Biostrings • reset
1
vote
4
replies
528
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 11 days ago by • 0
1
vote
3
replies
237
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 22 days ago by • 0
1
vote
1
reply
275
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
23 days ago • updated 22 days ago Gerhard Thallinger ▴ 180
0
votes
2
replies
460
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 10 weeks ago by • 0
0
votes
1
reply
450
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 6 weeks ago by ▴ 60 • written 7 weeks ago by • 0
4
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2
replies
541
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 3 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 5 months ago by 16k • written 5 months ago by • 0
3
votes
4
replies
550
views
Store output of matchPWM()
biostrings Biostrings
6 months ago • updated 5 months ago mat149 ▴ 80
0
votes
1
reply
361
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
888
views
From a DNAStringSet to a data.frame
Biostrings
7 months ago ramiro.barrantes ▴ 10
1
vote
5
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752
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 months ago • updated 7 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
308
views
How to search for a string in a DNAStringSet dataset?
Biostrings
9 months ago Angela Michalichyn • 0
2
votes
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
vote
3
replies
819
views
AAbin vs DNAbin structures
Biostrings
updated 14 months ago by 67k • written 14 months ago by • 0
0
votes
2
replies
935
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
votes
0
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529
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
21 months ago Gilles • 0
0
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0
replies
671
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
22 months ago Mario Dejung • 0
0
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0
replies
830
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
22 months ago vonSkopnik • 0
0
votes
2
replies
936
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 23 days ago by ▴ 20 • written 23 months ago by • 0
0
votes
0
replies
787
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
24 months ago biong • 0
0
votes
8
replies
1.5k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.0 years ago Brett • 0
3
votes
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
2.4k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.1 years ago Mog • 0
0
votes
1
reply
925
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.2 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
1.2k
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
2.6 years ago L ▴ 50
0
votes
4
replies
2.3k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.6 years ago by 67k • written 2.7 years ago by • 0
0
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0
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822
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.7 years ago vonSkopnik • 0
5
votes
5
replies
1.8k
views
Changing genetic_code_table in Biostrings
Biostrings
2.7 years ago Sam • 0
0
votes
0
replies
596
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.7 years ago Charles Plessy ▴ 180
0
votes
0
replies
799
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.7 years ago Charles Plessy ▴ 180
0
votes
2
replies
968
views
Simple subject extraction question with biostrings
Biostrings
2.8 years ago James • 0
1
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6
replies
1.9k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.8 years ago by 16k • written 2.9 years ago by ▴ 180
1
vote
2
replies
1.5k
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
3.0k
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
3.6k
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
942
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.2 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 3.4 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
3.6 years ago sieminsk • 0
3
votes
2
replies
2.2k
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
1.2k
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
3.9 years ago Bogdan ▴ 670
1
vote
1
reply
943
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.0 years ago by ▴ 10 • written 4.1 years ago by • 0
0
votes
0
replies
823
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.1 years ago jennyl.smith12 • 0
0
votes
3
replies
1.9k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.4 years ago by 67k • written 4.4 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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Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Ai • 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2 by icecreamlover • 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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