Showing : Biostrings • reset
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113
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Store output of matchPWM()
biostrings Biostrings
updated 1 day ago by 65k • written 1 day ago by ▴ 70
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1
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134
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
2
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2
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219
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From a DNAStringSet to a data.frame
Biostrings
5 weeks ago ramiro.barrantes ▴ 10
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5
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429
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
7 weeks ago • updated 6 weeks ago Gerhard Thallinger ▴ 180
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0
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158
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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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770
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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
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3
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527
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AAbin vs DNAbin structures
Biostrings
updated 7 months ago by 65k • written 8 months ago by • 0
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2
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701
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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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363
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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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480
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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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622
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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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676
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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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601
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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
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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
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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
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735
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Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 20 months ago by 16k • written 2.1 years ago by • 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 24 months ago by 16k • written 24 months ago by ▴ 10
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1
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972
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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
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979
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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
0
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0
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680
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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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470
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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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654
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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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761
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Simple subject extraction question with biostrings
Biostrings
2.3 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
2.5 years ago Madza Farias-Virgens • 0
2
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3
replies
2.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.5 years ago by 16k • written 2.5 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
2.5 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
0
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0
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764
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
2.7 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 2.9 years ago by 16k • written 2.9 years ago by ▴ 250
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0
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921
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
0
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3
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963
views
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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1.8k
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
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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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1.6k
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
783
views
Subset center regions of a set of different length sequences
Biostrings
updated 3.5 years ago by ▴ 10 • written 3.6 years ago by • 0
0
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0
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676
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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
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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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851
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
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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
3
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1
reply
960
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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0
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592
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Detect unique deletions in DNAMultipleAlignment
biostrings
4.0 years ago multipleseqs • 0
0
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2
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978
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
1
vote
2
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798
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.2 years ago by ★ 4.1k • written 4.3 years ago by ▴ 50
5
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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
716
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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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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