Showing : biostrings • reset
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3
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201
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AAbin vs DNAbin structures
Biostrings
updated 19 days ago by 63k • written 20 days ago by • 0
0
votes
2
replies
377
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 4 months ago by ▴ 70
0
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0
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176
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Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
7 months ago Gilles • 0
0
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0
replies
260
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
8 months ago Mario Dejung • 0
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0
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335
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
9 months ago vonSkopnik • 0
0
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1
reply
400
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Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
9 months ago 潘晓光 • 0
0
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0
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348
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
10 months ago biong • 0
0
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8
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760
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translate errors in fastq file reading
translate biostrings Biostrings
11 months ago Brett • 0
3
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5
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897
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Biostrings multiple pattern match
pattern Biostrings
updated 11 months ago by 16k • written 11 months ago by • 0
2
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2
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932
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
12 months ago • updated 11 months ago Mog • 0
0
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1
reply
503
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 13 months ago by 16k • written 17 months ago by • 0
0
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2
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868
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Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 16 months ago by 16k • written 16 months ago by ▴ 10
0
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1
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632
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 17 months ago by ▴ 720 • written 17 months ago by • 0
1
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0
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754
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
18 months ago L ▴ 50
0
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4
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1.3k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 18 months ago by 63k • written 18 months ago by • 0
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0
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474
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How to make a pairwiseAlignment of circular sequences
Biostrings
19 months ago vonSkopnik • 0
5
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5
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1.0k
views
Changing genetic_code_table in Biostrings
Biostrings
19 months ago Sam • 0
0
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0
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327
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
19 months ago Charles Plessy ▴ 180
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0
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454
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
19 months ago Charles Plessy ▴ 180
0
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2
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540
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Simple subject extraction question with biostrings
Biostrings
20 months ago James • 0
1
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6
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1.2k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 20 months ago by 16k • written 21 months ago by ▴ 180
1
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2
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911
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
22 months ago Madza Farias-Virgens • 0
2
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3
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1.8k
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How to get longest isoform
GenomicFeatures Biostrings
updated 22 months ago by 16k • written 22 months ago by • 0
1
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2
replies
706
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NAs in my txdb tx_name
GenomicFeatures Biostrings
22 months ago Madza Farias-Virgens • 0
0
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4
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2.3k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.1 years ago HELEN • 0
0
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0
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583
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.1 years ago emmanuel.verde2939 • 0
4
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9
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1.3k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 250
0
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0
replies
694
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
2.5 years ago adklts • 0
0
votes
3
replies
753
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
2.5 years ago sieminsk • 0
3
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2
replies
1.2k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
2.7 years ago Benjamin ▴ 20
2
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3
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758
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Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
2.8 years ago Nicholas Cooley • 0
6
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5
replies
1.2k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
2.8 years ago Bogdan ▴ 660
1
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1
reply
568
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Subset center regions of a set of different length sequences
Biostrings
updated 2.9 years ago by ▴ 10 • written 3.0 years ago by • 0
0
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0
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504
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.0 years ago jennyl.smith12 • 0
0
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3
replies
1.2k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 3.3 years ago by 63k • written 3.3 years ago by • 0
0
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4
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1.9k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
3.3 years ago moldach ▴ 20
1
vote
1
reply
658
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 3.3 years ago by 25k • written 3.3 years ago by ▴ 80
0
votes
3
replies
989
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 3.4 years ago by ▴ 290 • written 3.4 years ago by ▴ 80
3
votes
1
reply
700
views
Biostrings matchPattern with lower case
biostrings
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 20
0
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0
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438
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Detect unique deletions in DNAMultipleAlignment
biostrings
3.4 years ago multipleseqs • 0
0
votes
2
replies
718
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
3.5 years ago mb2subi • 0
1
vote
2
replies
589
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 3.6 years ago by ★ 3.4k • written 3.7 years ago by ▴ 50
5
votes
1
reply
2.5k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 3.7 years ago by ▴ 100 • written 3.7 years ago by ▴ 20
2
votes
1
reply
542
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 3.8 years ago by 16k • written 3.8 years ago by • 0
1
vote
1
reply
650
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 30
0
votes
1
reply
600
views
pairwisealignment how to normalize score?
biostrings
updated 3.9 years ago by 16k • written 3.9 years ago by • 0
0
votes
1
reply
814
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 3.9 years ago by 16k • written 3.9 years ago by • 0
1
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1
reply
465
views
Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
updated 3.9 years ago by 16k • written 3.9 years ago by • 0
1
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4
replies
1.4k
views
Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
4.3 years ago • updated 3.9 years ago daniel.magnus.bader ▴ 40
2
votes
3
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841
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.1 years ago by 3.5k • written 4.1 years ago by ▴ 160
50 results • Page 1 of 1
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Comment: Problems with FLOWAI by SHASHI • 0
please try this using short path name and keeping your fcs file and wsp file in your local directory https://youtu.be/xLeqE7PNYzA
Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Answer: Remove duplicates of colData in TreeSummarizedExperiment by Michael Love 40k
Copying my code from Slack for posterity. James' code is more streamlined for this step I think. ``` # make a dataset that has duplicate s…
Comment: DataFrame Construction With Non-standard Column by James W. MacDonald 63k
Oh, ok. I understand. Technically both should work according to what the help page for `DataFrame` says (both `SimpleList` and `list` have …
Votes
A: LIMMA dupcor() function time issue.
A: LIMMA dupcor() function time issue.
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Answer: DataFrame Construction With Non-standard Column
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