Showing : biostrings • reset
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 28 days ago by 65k • written 28 days ago by • 0
2
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2
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202
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From a DNAStringSet to a data.frame
Biostrings
4 weeks ago ramiro.barrantes ▴ 10
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5
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415
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
6 weeks ago • updated 5 weeks ago Gerhard Thallinger ▴ 180
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152
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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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754
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
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3
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507
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AAbin vs DNAbin structures
Biostrings
updated 7 months ago by 65k • written 7 months ago by • 0
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2
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684
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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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353
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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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467
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
15 months ago Mario Dejung • 0
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613
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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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670
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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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590
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
17 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
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Biostrings multiple pattern match
pattern Biostrings
updated 18 months ago by 16k • written 19 months ago by • 0
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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
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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 23 months ago by 16k • written 23 months ago by ▴ 10
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1
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961
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
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1
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727
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Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 20 months ago by 16k • written 2.0 years ago by • 0
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0
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961
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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
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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
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667
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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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465
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.2 years ago Charles Plessy ▴ 180
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647
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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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751
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Simple subject extraction question with biostrings
Biostrings
2.2 years ago James • 0
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6
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1.6k
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DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.3 years ago by 16k • written 2.4 years ago by ▴ 180
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2
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1.2k
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
2
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3
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2.5k
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How to get longest isoform
GenomicFeatures Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
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2
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1.0k
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NAs in my txdb tx_name
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
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4
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3.0k
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transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
2.7 years ago HELEN • 0
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0
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754
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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
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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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913
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.1 years ago adklts • 0
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3
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954
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DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.1 years ago sieminsk • 0
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2
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1.7k
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Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago Benjamin ▴ 20
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3
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997
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Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.4 years ago Nicholas Cooley • 0
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5
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1.5k
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to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
3.4 years ago Bogdan ▴ 670
1
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1
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777
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Subset center regions of a set of different length sequences
Biostrings
updated 3.5 years ago by ▴ 10 • written 3.5 years ago by • 0
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0
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665
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vcountPDict Out-of-Memory Errors
software error Biostrings
3.6 years ago jennyl.smith12 • 0
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3
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1.6k
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What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
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4
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2.3k
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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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842
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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
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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
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0
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587
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Detect unique deletions in DNAMultipleAlignment
biostrings
4.0 years ago multipleseqs • 0
3
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1
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948
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Biostrings matchPattern with lower case
biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 20
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2
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970
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
1
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2
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790
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searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 50
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1
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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
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1
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709
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
1
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1
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864
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Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 4.4 years ago by 25k • written 4.4 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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