Showing : BioStrings • reset
0
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1.1k
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vcountPDict Out-of-Memory Errors
software error Biostrings
5.2 years ago JennyS • 0
0
votes
3
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2.4k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
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4
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3.4k
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Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
5.6 years ago moldach ▴ 20
1
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1
reply
1.2k
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 90
0
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3
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1.9k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 5.7 years ago by ▴ 300 • written 5.7 years ago by ▴ 80
3
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1
reply
1.3k
views
Biostrings matchPattern with lower case
biostrings
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 20
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0
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837
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Detect unique deletions in DNAMultipleAlignment
biostrings
5.7 years ago multipleseqs • 0
0
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2
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1.4k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
5.7 years ago mb2subi • 0
1
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2
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1.3k
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 5.9 years ago by ★ 5.0k • written 5.9 years ago by ▴ 50
5
votes
1
reply
4.4k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 5.9 years ago by ▴ 110 • written 5.9 years ago by ▴ 20
2
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1
reply
1.0k
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 6.0 years ago by 16k • written 6.0 years ago by • 0
1
vote
1
reply
1.3k
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 6.0 years ago by 25k • written 6.0 years ago by ▴ 30
0
votes
1
reply
1.1k
views
pairwisealignment how to normalize score?
biostrings
updated 6.1 years ago by 16k • written 6.1 years ago by • 0
0
votes
1
reply
1.6k
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 6.1 years ago by 16k • written 6.1 years ago by • 0
1
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1
reply
960
views
Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
updated 6.1 years ago by 16k • written 6.1 years ago by • 0
1
vote
4
replies
2.4k
views
Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
6.5 years ago • updated 6.2 years ago daniel.magnus.bader ▴ 50
2
votes
3
replies
1.9k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 6.3 years ago by 4.2k • written 6.3 years ago by ▴ 160
2
votes
2
replies
1.3k
views
vcountPDict fails on PDict
Biostrings
updated 6.3 years ago by 16k • written 6.4 years ago by ▴ 160
4
votes
2
replies
2.7k
views
Biostrings regex matching
Biostrings
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 160
0
votes
6
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1.7k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
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0
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1.1k
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
6.6 years ago Juliet Hannah ▴ 360
0
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1
reply
939
views
Sensitivity and specificity in trimLRpatterns
Biostrings
6.8 years ago learoser • 0
6
votes
8
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4.0k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 90
3
votes
3
replies
1.9k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 120
2
votes
2
replies
1.4k
views
Using non standard charachters with XStrings object in BioStrings
BioStrings Inosine bases Hydroxyadenine Azobenzene IUPAC
updated 6.9 years ago by 16k • written 6.9 years ago by ▴ 20
0
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2
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2.2k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 6.9 years ago by 0 • written 16.9 years ago by ★ 1.9k
1
vote
3
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1.6k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ★ 3.4k
0
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2
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1.9k
views
Biostrings: revComp error: Not compatible with STRSXP
biostrings Error Not compatible with STRSXP
7.0 years ago camille.4nier • 0
0
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2
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1.6k
views
Biostrings install error
biostrings install error
7.1 years ago owenchapman1 • 0
0
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4
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1.9k
views
Biostrings - translate gives wrong results for triplets TTG and CTG
biostrings
updated 7.1 years ago by 16k • written 7.5 years ago by • 0
0
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0
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867
views
alphabet/encoding IlluminaQuality SolexaQuality
Biostrings XStringQuality
7.1 years ago felix.ernst • 0
1
vote
3
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2.2k
views
Remove reads from raw fastq
shortread biostrings
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
3
votes
2
replies
5.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
0
votes
4
replies
5.6k
views
Retrieving specific sequences from a fastq
shortread biostrings
7.2 years ago ferbecneu • 0
0
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0
replies
1.6k
views
Match peptide within protein sequence fasta and extract position information based on protein sequence
R seqinr biostrings
7.3 years ago rabalski • 0
0
votes
2
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1.7k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 7.3 years ago by 16k • written 7.3 years ago by • 0
0
votes
1
reply
1.4k
views
Cannot Update Biostrings to Latest Version
dada2 biostrings
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
2
votes
2
replies
1.1k
views
Biostrings: "Error in .normargSEW(start, "start")"
Biostrings
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 120
0
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2
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1.0k
views
Support for BSgenomeViews objects in matchPWM
biostrings
7.6 years ago s1437643 ▴ 20
0
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1
reply
1.1k
views
Biostrings translate alt_init_codons, rule doesn't apply, how to get rid of the attribution
biostrings translate
7.7 years ago XIA.PAN ▴ 20
1
vote
1
reply
1.5k
views
Bug in Biostrings DNAStringSet(), segfault
bug biostrings
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 10
2
votes
2
replies
2.8k
views
How to combine sequences from different stringsets?
biostrings decipher
updated 7.9 years ago by ★ 6.6k • written 7.9 years ago by • 0
0
votes
1
reply
885
views
Unexpected behavior in Biostrings::pairwiseAlignment
biostrings
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
0
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3
replies
2.0k
views
How to find multiple overlaps with pairwiseAlignment()?
biostrings pairwisealignment
updated 7.9 years ago by 16k • written 7.9 years ago by ▴ 10
2
votes
1
reply
1.4k
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 7.9 years ago by 4.2k • written 7.9 years ago by ▴ 10
0
votes
2
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1.2k
views
Error in pairwiseAlignment when considering an empty seuqnece
biostrings
updated 7.9 years ago by 16k • written 9.5 years ago by ▴ 20
5
votes
7
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2.4k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by • 0
0
votes
2
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1.5k
views
Is it possible to import many .tsr sequence file into R using bio strings for use in DECIPHER?
r biostrings decipher
8.0 years ago reubenmcgregor88 • 0
2
votes
5
replies
2.5k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 8.0 years ago by ▴ 150 • written 8.0 years ago by • 0
2
votes
3
replies
2.5k
views
Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher DNA biostrings
updated 8.0 years ago by ▴ 150 • written 8.0 years ago by • 0
292 results • Page 2 of 6
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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