Showing : Biostrings • reset
3
votes
4
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273
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Store output of matchPWM()
biostrings Biostrings
16 days ago • updated 4 days ago mat149 ▴ 70
0
votes
1
reply
155
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
2
votes
2
replies
256
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From a DNAStringSet to a data.frame
Biostrings
7 weeks ago ramiro.barrantes ▴ 10
1
vote
5
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458
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
10 weeks ago • updated 8 weeks ago Gerhard Thallinger ▴ 180
0
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0
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175
views
How to search for a string in a DNAStringSet dataset?
Biostrings
4 months ago Angela Michalichyn • 0
2
votes
6
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796
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
1
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3
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553
views
AAbin vs DNAbin structures
Biostrings
updated 8 months ago by 65k • written 8 months ago by • 0
0
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2
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721
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
0
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0
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376
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
15 months ago Gilles • 0
0
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0
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491
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
16 months ago Mario Dejung • 0
0
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0
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629
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
16 months ago vonSkopnik • 0
0
votes
1
reply
686
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
17 months ago 潘晓光 • 0
0
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0
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610
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
18 months ago biong • 0
0
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8
replies
1.2k
views
translate errors in fastq file reading
translate biostrings Biostrings
18 months ago Brett • 0
3
votes
5
replies
1.5k
views
Biostrings multiple pattern match
pattern Biostrings
updated 19 months ago by 16k • written 19 months ago by • 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
0
votes
1
reply
746
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 21 months ago by 16k • written 2.1 years ago by • 0
0
votes
2
replies
1.3k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.0 years ago by 16k • written 2.0 years ago by ▴ 10
0
votes
1
reply
987
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
vote
0
replies
1.0k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.2 years ago L ▴ 50
0
votes
4
replies
1.9k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
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0
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691
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.2 years ago vonSkopnik • 0
5
votes
5
replies
1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.2 years ago Sam • 0
0
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0
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479
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.3 years ago Charles Plessy ▴ 180
0
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0
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664
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.3 years ago Charles Plessy ▴ 180
0
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2
replies
777
views
Simple subject extraction question with biostrings
Biostrings
2.3 years ago James • 0
1
vote
6
replies
1.6k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 180
1
vote
2
replies
1.3k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
votes
3
replies
2.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
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2
replies
1.0k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.1k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.7 years ago HELEN • 0
0
votes
0
replies
775
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.8 years ago emmanuel.verde2939 • 0
4
votes
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 3.0 years ago by ▴ 250
0
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0
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940
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
0
votes
3
replies
979
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.2 years ago • updated 3.1 years ago sieminsk • 0
3
votes
2
replies
1.8k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago Benjamin ▴ 20
2
votes
3
replies
1.0k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
6
votes
5
replies
1.6k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.5 years ago Bogdan ▴ 670
1
vote
1
reply
792
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.6 years ago by ▴ 10 • written 3.6 years ago by • 0
0
votes
0
replies
689
views
vcountPDict Out-of-Memory Errors
software error Biostrings
3.7 years ago jennyl.smith12 • 0
0
votes
3
replies
1.6k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
0
votes
4
replies
2.3k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.0 years ago moldach ▴ 20
1
vote
1
reply
863
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 90
0
votes
3
replies
1.3k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.1 years ago by ▴ 290 • written 4.1 years ago by ▴ 80
3
votes
1
reply
982
views
Biostrings matchPattern with lower case
biostrings
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 20
0
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0
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600
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.1 years ago multipleseqs • 0
0
votes
2
replies
991
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
1
vote
2
replies
811
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.3 years ago by ★ 4.1k • written 4.3 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 4.4 years ago by ▴ 100 • written 4.4 years ago by ▴ 20
2
votes
1
reply
727
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
50 results • Page 1 of 1
Recent ...
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Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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