Showing : Biostrings • reset
2
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3
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Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 29 days ago by 16k • written 4 weeks ago by • 0
3
votes
4
replies
358
views
Store output of matchPWM()
biostrings Biostrings
8 weeks ago • updated 6 weeks ago mat149 ▴ 80
0
votes
1
reply
211
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 3 months ago by 66k • written 3 months ago by • 0
2
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2
replies
406
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From a DNAStringSet to a data.frame
Biostrings
3 months ago ramiro.barrantes ▴ 10
1
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5
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543
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
3 months ago Gerhard Thallinger ▴ 180
0
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0
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201
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How to search for a string in a DNAStringSet dataset?
Biostrings
5 months ago Angela Michalichyn • 0
2
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6
replies
858
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 8 months ago by 16k • written 9 months ago by • 0
1
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3
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615
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AAbin vs DNAbin structures
Biostrings
updated 9 months ago by 66k • written 9 months ago by • 0
0
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2
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761
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 14 months ago by ▴ 70
0
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0
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407
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Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
16 months ago Gilles • 0
0
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0
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519
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
17 months ago Mario Dejung • 0
0
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0
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665
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
18 months ago vonSkopnik • 0
0
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1
reply
726
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
18 months ago 潘晓光 • 0
0
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0
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639
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
19 months ago biong • 0
0
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8
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1.3k
views
translate errors in fastq file reading
translate biostrings Biostrings
20 months ago Brett • 0
3
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5
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1.6k
views
Biostrings multiple pattern match
pattern Biostrings
updated 21 months ago by 16k • written 21 months ago by • 0
2
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2
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2.0k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
21 months ago Mog • 0
0
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1
reply
778
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 22 months ago by 16k • written 2.2 years ago by • 0
0
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2
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1.4k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.1 years ago by 16k • written 2.1 years ago by ▴ 10
0
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1
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1.0k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
1
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0
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1.1k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.3 years ago L ▴ 50
0
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4
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2.0k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.3 years ago by 66k • written 2.3 years ago by • 0
0
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0
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720
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How to make a pairwiseAlignment of circular sequences
Biostrings
2.3 years ago vonSkopnik • 0
5
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5
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1.6k
views
Changing genetic_code_table in Biostrings
Biostrings
2.4 years ago Sam • 0
0
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0
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505
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.4 years ago Charles Plessy ▴ 180
0
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0
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693
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.4 years ago Charles Plessy ▴ 180
0
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2
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816
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Simple subject extraction question with biostrings
Biostrings
2.4 years ago James • 0
1
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6
replies
1.7k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.5 years ago by 16k • written 2.6 years ago by ▴ 180
1
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2
replies
1.3k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.6 years ago Madza Farias-Virgens • 0
2
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3
replies
2.7k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
1
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2
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1.1k
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NAs in my txdb tx_name
GenomicFeatures Biostrings
2.6 years ago Madza Farias-Virgens • 0
0
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4
replies
3.2k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.8 years ago HELEN • 0
0
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0
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805
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Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.9 years ago emmanuel.verde2939 • 0
4
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9
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1.8k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 250
0
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0
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975
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.2 years ago adklts • 0
0
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3
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1.0k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.3 years ago • updated 3.2 years ago sieminsk • 0
3
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2
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1.9k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.5 years ago • updated 3.4 years ago Benjamin ▴ 20
2
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3
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1.1k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.5 years ago Nicholas Cooley • 0
6
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5
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1.7k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.6 years ago Bogdan ▴ 670
1
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1
reply
823
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Subset center regions of a set of different length sequences
Biostrings
updated 3.7 years ago by ▴ 10 • written 3.7 years ago by • 0
0
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0
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716
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.8 years ago jennyl.smith12 • 0
0
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3
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1.7k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.1 years ago by 66k • written 4.1 years ago by • 0
0
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4
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2.4k
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Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.1 years ago moldach ▴ 20
1
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1
reply
893
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 4.1 years ago by 25k • written 4.1 years ago by ▴ 90
0
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3
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1.4k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.2 years ago by ▴ 290 • written 4.2 years ago by ▴ 80
3
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1
reply
1.0k
views
Biostrings matchPattern with lower case
biostrings
updated 4.2 years ago by 16k • written 4.2 years ago by ▴ 20
0
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0
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621
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Detect unique deletions in DNAMultipleAlignment
biostrings
4.2 years ago multipleseqs • 0
0
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2
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1.0k
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.2 years ago mb2subi • 0
1
vote
2
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845
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.4 years ago by ★ 4.2k • written 4.4 years ago by ▴ 50
5
votes
1
reply
3.2k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 4.5 years ago by ▴ 100 • written 4.5 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: Ranking the GSEA Results by Michael Love 42k
Some posts on this topic: https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR by Gordon Smyth 51k
edgeR allows observation specific offsets (as already pointed out), although I am not confident that would be a reliable solution to your p…
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
Thank you I will take a look at those !
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
I will send you an email and talk to my advisor about setting up a meeting. Thank you !
Comment: Research Project - Expanding search funtionality on the GEO database by Sean Davis 21k
You can use the Bioconductor Annotation packages for the Affymetrix chips of interest. - https://bioconductor.org/packages/release/BiocVie…
Votes
Answer: DESeq2 time course using fitted splines
Answer: DESeq2 time course using fitted splines
Comment: Difference between enrichGO results and Enrichr website results
Answer: Struggling to convert a large list of non-model genes into human orthologs, any
A: makeContrasts from limma overides "i" as a varible
Awards • All
Popular Question to Gordon Smyth 51k
Popular Question to Sean Davis 21k
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Martin Morgan 25k
Popular Question to Wolfgang Huber ★ 13k
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