Showing : biostrings • reset
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 22 days ago by 65k • written 22 days ago by • 0
2
votes
2
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190
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From a DNAStringSet to a data.frame
Biostrings
24 days ago • updated 23 days ago ramiro.barrantes ▴ 10
1
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5
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403
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Biostrings: read*StringSet() functions leave open file handles
Biostrings
6 weeks ago • updated 4 weeks ago Gerhard Thallinger ▴ 180
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0
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145
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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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745
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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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487
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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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669
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 11 months ago by ▴ 70
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345
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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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459
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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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605
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
15 months ago vonSkopnik • 0
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1
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659
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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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584
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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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1.1k
views
translate errors in fastq file reading
translate biostrings Biostrings
17 months ago Brett • 0
3
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5
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1.4k
views
Biostrings multiple pattern match
pattern Biostrings
updated 18 months ago by 16k • written 18 months ago by • 0
2
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2
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1.7k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
18 months ago Mog • 0
0
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1
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719
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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
1
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9
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2.4k
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Handling DNA sequence loaded from a file
r biostrings DNAsequence
updated 22 months ago by 65k • written 8.0 years ago by ▴ 260
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2
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1.2k
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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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947
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.0 years ago by ▴ 770 • written 2.0 years ago by • 0
1
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0
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947
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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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0
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659
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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
0
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0
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458
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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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637
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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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745
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Simple subject extraction question with biostrings
Biostrings
2.2 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
2.4 years ago Madza Farias-Virgens • 0
2
votes
3
replies
2.4k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
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2
replies
995
views
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
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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747
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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1.6k
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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3
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941
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DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.1 years ago • updated 3.0 years ago sieminsk • 0
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0
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904
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.0 years ago adklts • 0
3
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2
replies
1.7k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.3 years ago • updated 3.2 years ago Benjamin ▴ 20
0
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5
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2.5k
views
How to prevent readDNAStringSet() function from switching masked sequences (lowercase) to uppercase sequence?
biostrings mask repeatmasker DNA
updated 3.2 years ago by • 0 • written 6.4 years ago by • 0
2
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3
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989
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
3.3 years ago Nicholas Cooley • 0
6
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5
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1.5k
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
770
views
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
0
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0
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659
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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
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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
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
reply
838
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
0
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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
votes
1
reply
940
views
Biostrings matchPattern with lower case
biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 20
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0
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581
views
Detect unique deletions in DNAMultipleAlignment
biostrings
4.0 years ago multipleseqs • 0
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2
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964
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.0 years ago mb2subi • 0
1
vote
2
replies
785
views
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
5
votes
1
reply
3.0k
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
50 results • Page 1 of 1
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Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR by Gordon Smyth 50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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