Showing : Biostrings • reset
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Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 3 days ago by 15k • written 3 days ago by ▴ 10
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1
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81
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 4 weeks ago by ▴ 280 • written 4 weeks ago by • 0
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0
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49
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Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
4 weeks ago James • 0
1
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0
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95
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
8 weeks ago L • 0
0
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4
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201
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Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 8 weeks ago by 59k • written 9 weeks ago by • 0
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0
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124
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How to make a pairwiseAlignment of circular sequences
Biostrings
11 weeks ago vonSkopnik • 0
5
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5
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328
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Changing genetic_code_table in Biostrings
Biostrings
12 weeks ago Sam • 0
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0
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70
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
12 weeks ago Charles Plessy ▴ 170
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76
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
3 months ago Charles Plessy ▴ 170
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2
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125
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Simple subject extraction question with biostrings
Biostrings
3 months ago James • 0
1
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6
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450
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DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 4 months ago by 15k • written 5 months ago by ▴ 180
1
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2
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323
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
6 months ago • updated 5 months ago Madza Farias-Virgens • 0
2
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3
replies
361
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How to get longest isoform
GenomicFeatures Biostrings
updated 6 months ago by 15k • written 6 months ago by • 0
1
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2
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256
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NAs in my txdb tx_name
GenomicFeatures Biostrings
6 months ago Madza Farias-Virgens • 0
0
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4
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699
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transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
8 months ago HELEN • 0
0
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0
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197
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Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
9 months ago emmanuel.verde2939 • 0
4
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9
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614
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How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 11 months ago by 15k • written 11 months ago by ▴ 180
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0
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277
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
13 months ago adklts • 0
0
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3
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392
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DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
13 months ago sieminsk • 0
3
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2
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396
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Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
16 months ago • updated 15 months ago Benjamin ▴ 20
2
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3
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353
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Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
17 months ago Nicholas Cooley • 0
6
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5
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626
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to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
17 months ago Bogdan ▴ 640
1
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1
reply
294
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Subset center regions of a set of different length sequences
Biostrings
updated 19 months ago by ▴ 10 • written 19 months ago by • 0
0
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0
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234
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vcountPDict Out-of-Memory Errors
software error Biostrings
20 months ago jennyl.smith12 • 0
0
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3
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601
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What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 23 months ago by 59k • written 23 months ago by • 0
0
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4
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862
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Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
24 months ago moldach ▴ 20
1
vote
1
reply
328
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 24 months ago by 25k • written 24 months ago by ▴ 80
0
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3
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439
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 2.1 years ago by ▴ 290 • written 2.1 years ago by ▴ 70
3
votes
1
reply
297
views
Biostrings matchPattern with lower case
biostrings
updated 2.1 years ago by 15k • written 2.1 years ago by ▴ 10
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0
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201
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Detect unique deletions in DNAMultipleAlignment
biostrings
2.1 years ago multipleseqs • 0
0
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2
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348
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
2.1 years ago mb2subi • 0
1
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2
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279
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 2.3 years ago by ★ 1.2k • written 2.3 years ago by ▴ 50
3
votes
1
reply
1.0k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 2.3 years ago by ▴ 90 • written 2.3 years ago by ▴ 10
2
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1
reply
274
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 2.4 years ago by 15k • written 2.4 years ago by • 0
1
vote
1
reply
349
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 2.4 years ago by 25k • written 2.4 years ago by ▴ 30
0
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1
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318
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pairwisealignment how to normalize score?
biostrings
updated 2.5 years ago by 15k • written 2.5 years ago by • 0
0
votes
1
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444
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 2.5 years ago by 15k • written 2.5 years ago by • 0
1
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1
reply
258
views
Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
updated 2.6 years ago by 15k • written 2.6 years ago by • 0
1
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4
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783
views
Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
2.9 years ago • updated 2.6 years ago daniel.magnus.bader ▴ 40
2
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3
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379
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What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 2.7 years ago by 3.1k • written 2.7 years ago by ▴ 140
2
votes
2
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373
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vcountPDict fails on PDict
Biostrings
updated 2.8 years ago by 15k • written 2.8 years ago by ▴ 140
4
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2
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1.0k
views
Biostrings regex matching
Biostrings
updated 2.9 years ago by 15k • written 2.9 years ago by ▴ 140
0
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6
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497
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error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 3.0 years ago by 59k • written 3.0 years ago by • 0
0
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0
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343
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
3.0 years ago Juliet Hannah ▴ 360
0
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1
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397
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Sensitivity and specificity in trimLRpatterns
Biostrings
3.2 years ago learoser • 0
5
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8
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1.3k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 3.2 years ago by 25k • written 3.2 years ago by ▴ 70
3
votes
3
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661
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 3.3 years ago by 11k • written 3.3 years ago by ▴ 100
2
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2
replies
590
views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
updated 3.3 years ago by 15k • written 3.3 years ago by ▴ 20
0
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2
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1.2k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 3.3 years ago by 0 • written 13.3 years ago by ★ 1.9k
1
vote
3
replies
611
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Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 3.4 years ago by 11k • written 3.4 years ago by ★ 2.8k
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by karenserrano • 0
Hi Johannes, Could I request the same EnsDb creation for Medicago truncatula? Thank you very much, Karen
Answer: EnrichGO not working with db created from annotationhub by Guido Hooiveld ★ 3.2k
Did you notice the first message that was returned after you ran `enrichGO()`? Thus: `--> No gene can be mapped....` This basically means…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by ksong • 0
Hello my friends, I have exactly the same issue. May I ask if you have already solve this problem? I have tried `library(BiocParallel) regi…
Comment: cellCounts() function floating point error by Wei Shi ★ 3.3k
Yes we are currently working on generating a small example for cellCounts.
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU by ksong • 0
Hi Dr Sudbery, yes I found looking at the coverage in IGV helps a lot. I did find some differences between CDS and UTR and between samples.…
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Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
Comment: Diffbind dba$binding slot finding Chr21 for an MM10 dataset
Answer: Handling NA values in limma's voom design matrix
Answer: Handling NA values in limma's voom design matrix
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