Showing : biostrings • reset
3
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4
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275
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Store output of matchPWM()
biostrings Biostrings
17 days ago • updated 5 days ago mat149 ▴ 70
0
votes
1
reply
159
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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
259
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From a DNAStringSet to a data.frame
Biostrings
7 weeks ago ramiro.barrantes ▴ 10
1
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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
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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
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796
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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
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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
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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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0
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376
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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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631
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
16 months ago vonSkopnik • 0
0
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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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611
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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
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1.2k
views
translate errors in fastq file reading
translate biostrings Biostrings
18 months ago Brett • 0
3
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5
replies
1.5k
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
replies
1.8k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
0
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1
reply
746
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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
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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
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4
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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
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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
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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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665
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.3 years ago Charles Plessy ▴ 180
0
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2
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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
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776
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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941
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
0
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3
replies
980
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
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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
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2
replies
991
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
1
vote
2
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812
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
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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…
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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