Showing : Biostrings • reset
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
4 weeks ago sandmann.t ▴ 70
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88
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Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
3 months ago Gilles • 0
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0
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147
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adding peptides to a multiple sequence alignment
msa IRanges Biostrings
4 months ago Mario Dejung • 0
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212
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
5 months ago vonSkopnik • 0
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1
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272
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Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
5 months ago 潘晓光 • 0
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206
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how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
6 months ago biong • 0
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8
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578
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translate errors in fastq file reading
translate biostrings Biostrings
7 months ago Brett • 0
3
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5
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676
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Biostrings multiple pattern match
pattern Biostrings
updated 8 months ago by 16k • written 8 months ago by • 0
2
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2
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643
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
8 months ago Mog • 0
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1
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393
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Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 9 months ago by 16k • written 13 months ago by • 0
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2
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662
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Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 12 months ago by 16k • written 12 months ago by ▴ 10
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1
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500
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 13 months ago by ▴ 720 • written 13 months ago by • 0
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593
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
14 months ago L ▴ 50
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4
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993
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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 14 months ago by 63k • written 14 months ago by • 0
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384
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How to make a pairwiseAlignment of circular sequences
Biostrings
15 months ago vonSkopnik • 0
5
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5
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886
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Changing genetic_code_table in Biostrings
Biostrings
15 months ago Sam • 0
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264
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Text display of entire `DNAMultipleAlignment` objects
Biostrings
15 months ago Charles Plessy ▴ 170
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330
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
16 months ago Charles Plessy ▴ 170
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2
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419
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Simple subject extraction question with biostrings
Biostrings
16 months ago James • 0
1
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6
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1.0k
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DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 17 months ago by 16k • written 18 months ago by ▴ 180
1
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2
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751
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
18 months ago Madza Farias-Virgens • 0
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3
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1.4k
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How to get longest isoform
GenomicFeatures Biostrings
updated 18 months ago by 16k • written 18 months ago by • 0
1
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2
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569
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NAs in my txdb tx_name
GenomicFeatures Biostrings
18 months ago Madza Farias-Virgens • 0
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4
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2.0k
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transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
21 months ago HELEN • 0
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0
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480
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Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
22 months ago emmanuel.verde2939 • 0
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9
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1.1k
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How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 24 months ago by 16k • written 2.0 years ago by ▴ 250
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582
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matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
2.2 years ago adklts • 0
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3
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661
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
2.2 years ago sieminsk • 0
3
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2
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956
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
2.4 years ago Benjamin ▴ 20
2
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3
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672
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Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
2.5 years ago Nicholas Cooley • 0
6
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5
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1.1k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
2.5 years ago Bogdan ▴ 660
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1
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503
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Subset center regions of a set of different length sequences
Biostrings
updated 2.6 years ago by ▴ 10 • written 2.6 years ago by • 0
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444
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vcountPDict Out-of-Memory Errors
software error Biostrings
2.7 years ago jennyl.smith12 • 0
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3
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1.1k
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What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
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4
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1.6k
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Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
3.0 years ago moldach ▴ 20
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1
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574
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Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 3.0 years ago by 25k • written 3.0 years ago by ▴ 80
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3
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860
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Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 3.1 years ago by ▴ 290 • written 3.1 years ago by ▴ 80
3
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1
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561
views
Biostrings matchPattern with lower case
biostrings
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 20
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0
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368
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Detect unique deletions in DNAMultipleAlignment
biostrings
3.1 years ago multipleseqs • 0
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2
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580
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
3.2 years ago mb2subi • 0
1
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2
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502
views
searching siRNA sequence (19bp) against human genome
searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern
updated 3.3 years ago by ★ 2.9k • written 3.3 years ago by ▴ 50
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1
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2.3k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 3.4 years ago by ▴ 100 • written 3.4 years ago by ▴ 20
2
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1
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428
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Move DNAString to the top of the DNAStringSet
Biostrings Bioconductor
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
1
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1
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566
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Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
Biostrings
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 30
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1
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500
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pairwisealignment how to normalize score?
biostrings
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
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1
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715
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Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
1
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1
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413
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Tabulating instances of letter combinations in strings.
Biostrings alphabetFrequency letterFrequency
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
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4
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1.3k
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Embedded nul \0 in string with Biostrings::readAAStringSet()
Biostrings
4.0 years ago • updated 3.6 years ago daniel.magnus.bader ▴ 40
2
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3
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677
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What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 3.7 years ago by 3.5k • written 3.8 years ago by ▴ 160
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2
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627
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vcountPDict fails on PDict
Biostrings
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 160
50 results • Page 1 of 1
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Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Comment: Interpret plot from DiffBind by Chris • 0
Thank you for the explanation! The purple (**gain**) in the control in the right bottom corner but on the y axis is labeled **loss** which …
Comment: Use with_go along with other filters in getBM function by RuBBiT0 ▴ 10
Thank you! I think that makes much sense to me.
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …
Comment: Interpret plot from DiffBind by Chris • 0
Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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