Showing : Biostrings • reset
2
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3
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1.1k
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Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 16 days ago by 16k • written 20 days ago by • 0
3
votes
4
replies
342
views
Store output of matchPWM()
biostrings Biostrings
6 weeks ago • updated 4 weeks ago mat149 ▴ 80
0
votes
1
reply
196
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 11 weeks ago by 66k • written 11 weeks ago by • 0
2
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2
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359
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From a DNAStringSet to a data.frame
Biostrings
11 weeks ago ramiro.barrantes ▴ 10
1
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5
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517
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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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193
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How to search for a string in a DNAStringSet dataset?
Biostrings
4 months ago Angela Michalichyn • 0
2
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6
replies
838
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 8 months ago by 16k • written 8 months ago by • 0
1
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3
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597
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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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741
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 13 months ago by ▴ 70
0
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0
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400
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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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511
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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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656
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
17 months ago vonSkopnik • 0
0
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1
reply
712
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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630
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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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1.2k
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translate errors in fastq file reading
translate biostrings Biostrings
19 months ago Brett • 0
3
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5
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1.5k
views
Biostrings multiple pattern match
pattern Biostrings
updated 20 months ago by 16k • written 20 months ago by • 0
2
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2
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1.9k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
20 months ago Mog • 0
0
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1
reply
769
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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1.0k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.2 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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710
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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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1.5k
views
Changing genetic_code_table in Biostrings
Biostrings
2.3 years ago Sam • 0
0
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0
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497
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.3 years ago Charles Plessy ▴ 180
0
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0
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682
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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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802
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Simple subject extraction question with biostrings
Biostrings
2.4 years ago James • 0
1
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6
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1.7k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.4 years ago by 16k • written 2.5 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
2.6 years ago Madza Farias-Virgens • 0
2
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3
replies
2.6k
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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795
views
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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1.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.0 years ago by 16k • written 3.1 years ago by ▴ 250
0
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0
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964
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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
replies
1.0k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
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
3.4 years ago Benjamin ▴ 20
2
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3
replies
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
3.5 years ago Bogdan ▴ 670
1
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1
reply
809
views
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
replies
705
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.7 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 4.0 years ago by 66k • written 4.0 years ago by • 0
0
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4
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2.4k
views
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
885
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
votes
3
replies
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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611
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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
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.2 years ago mb2subi • 0
1
vote
2
replies
832
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 4.4 years ago by ▴ 100 • written 4.4 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Awards • All
Popular Question to swbarnes2 ★ 1.4k
Popular Question to Stephanie M. Gogarten ▴ 870
Popular Question to Jonathan ▴ 10
Popular Question to Frederico Moraes Ferreira ▴ 100
Popular Question to richardallenfriedmanbrooklyn ▴ 20
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