Showing : BioStrings • reset
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119
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 29 days ago by 65k • written 29 days ago by • 0
2
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2
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203
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From a DNAStringSet to a data.frame
Biostrings
4 weeks ago ramiro.barrantes ▴ 10
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5
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419
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
7 weeks ago • updated 5 weeks ago Gerhard Thallinger ▴ 180
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0
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152
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How to search for a string in a DNAStringSet dataset?
Biostrings
3 months ago Angela Michalichyn • 0
2
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6
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758
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
1
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3
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509
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AAbin vs DNAbin structures
Biostrings
updated 7 months ago by 65k • written 7 months ago by • 0
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2
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688
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
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356
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Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
14 months ago Gilles • 0
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0
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469
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
15 months ago Mario Dejung • 0
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0
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615
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
16 months ago vonSkopnik • 0
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1
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672
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Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
16 months ago 潘晓光 • 0
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0
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590
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
17 months ago biong • 0
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8
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1.2k
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translate errors in fastq file reading
translate biostrings Biostrings
18 months ago Brett • 0
3
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5
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1.4k
views
Biostrings multiple pattern match
pattern Biostrings
updated 19 months ago by 16k • written 19 months ago by • 0
2
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2
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1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
0
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2
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1.3k
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Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 23 months ago by 16k • written 23 months ago by ▴ 10
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1
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961
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
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1
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727
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Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 20 months ago by 16k • written 2.0 years ago by • 0
1
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0
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966
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.1 years ago L ▴ 50
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4
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1.8k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
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0
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668
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How to make a pairwiseAlignment of circular sequences
Biostrings
2.2 years ago vonSkopnik • 0
5
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5
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1.4k
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Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago Sam • 0
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0
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465
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.2 years ago Charles Plessy ▴ 180
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0
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648
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.2 years ago Charles Plessy ▴ 180
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2
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752
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Simple subject extraction question with biostrings
Biostrings
2.2 years ago James • 0
1
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6
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1.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.3 years ago by 16k • written 2.4 years ago by ▴ 180
1
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2
replies
1.2k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
2
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3
replies
2.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
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2
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1.0k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
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4
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3.0k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.7 years ago HELEN • 0
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0
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756
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Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.7 years ago emmanuel.verde2939 • 0
4
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9
replies
1.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 250
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0
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917
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
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3
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959
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DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.1 years ago sieminsk • 0
3
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2
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1.7k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago Benjamin ▴ 20
2
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3
replies
1.0k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
6
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5
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1.5k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago Bogdan ▴ 670
1
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1
reply
778
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.5 years ago by ▴ 10 • written 3.5 years ago by • 0
0
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0
replies
668
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.6 years ago jennyl.smith12 • 0
0
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3
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1.6k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
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4
replies
2.3k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
3.9 years ago moldach ▴ 20
1
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1
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843
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 90
0
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3
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1.3k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.0 years ago by ▴ 290 • written 4.0 years ago by ▴ 80
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0
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588
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.0 years ago multipleseqs • 0
3
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1
reply
951
views
Biostrings matchPattern with lower case
biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 20
0
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2
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972
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
1
vote
2
replies
791
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 50
5
votes
1
reply
3.1k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 4.3 years ago by ▴ 100 • written 4.3 years ago by ▴ 20
2
votes
1
reply
711
views
Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 4.4 years ago by 16k • written 4.4 years ago by • 0
1
vote
1
reply
866
views
Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 4.4 years ago by 25k • written 4.4 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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