Showing : Biostrings • reset
0
votes
4
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1.9k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
0
votes
1
reply
1.5k
views
Using letterFrequencyInSlidingView with an AAStringSet
biostrings aastringset letterFrequencyInSlidingView xstringset
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
0
votes
5
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3.2k
views
How to prevent readDNAStringSet() function from switching masked sequences (lowercase) to uppercase sequence?
biostrings mask repeatmasker DNA
updated 4.8 years ago by • 0 • written 8.0 years ago by • 0
2
votes
2
replies
3.5k
views
msa: How to obtain a subset of an alignment
msa Biostrings MultipleAlignment
updated 8.1 years ago by ▴ 300 • written 8.1 years ago by ▴ 10
1
vote
2
replies
1.7k
views
untranslate AAstringset {Biostrings} or MsaAAMultipleAlignment {msa}
biostrings msa
8.2 years ago multipleseqs • 0
2
votes
8
replies
2.7k
views
CAGEr BAM files size issue
CAGEr BAM software error R biostrings
updated 8.2 years ago by ▴ 180 • written 8.3 years ago by ▴ 10
0
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0
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1.3k
views
biostrings report "XStringSet object is too big to be unlisted" error
Biostrings
8.2 years ago zwfanwz678 • 0
0
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0
replies
1.4k
views
How to run a CDHIT command of "BioSeqClass" package on DNAStringSet object of DNA sequences to get non-redundent set of sequences?
CD-HIT BioStrings cdhit biostrings BioSeqClass
8.3 years ago vinod.acear ▴ 50
0
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2
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1.5k
views
Human reference primary assembly and masking using BioStrings and BSgenome
biostrings R bsgenome
8.3 years ago rockyb • 0
2
votes
4
replies
4.2k
views
Biostrings translate() function with alternative genetic code is not working for first codon
biostrings genetic code translate
updated 8.4 years ago by 16k • written 8.4 years ago by • 0
1
vote
7
replies
3.2k
views
Mapping Probes to a Genome
BSgenome biostrings probe mapping
updated 8.5 years ago by ▴ 10 • written 9.2 years ago by ★ 1.6k
0
votes
1
reply
2.9k
views
Subsetting/subsequencing AAStringSet containing sequences of unequal length
biostrings aastringset subsetting
updated 8.5 years ago by 16k • written 8.5 years ago by • 0
5
votes
4
replies
3.4k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 8.5 years ago by 16k • written 8.5 years ago by ▴ 70
2
votes
4
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5.6k
views
What is the best way to subset a DNAStringSet by a GRange ?
bioconductor biostrings granges
updated 8.5 years ago by ★ 11k • written 8.5 years ago by • 0
0
votes
2
replies
3.0k
views
Biostrings: retrieve 3'UTR sequence with Transcript
R Biostrings sequence
updated 8.6 years ago by ★ 6.6k • written 8.6 years ago by • 0
1
vote
1
reply
953
views
Cannot replace subset of DNAStringSet object
biostrings
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
2
votes
4
replies
1.7k
views
Ranges on AAStrings
AAString Views Biostrings
8.7 years ago tobias.kockmann ▴ 20
4
votes
7
replies
2.2k
views
how to catch an error when using subseq() in vectorized way
biostrings subseq
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 20
0
votes
1
reply
1.4k
views
creating PDIct from AAStringSets
PDict Biostrings aastring
updated 8.7 years ago by 16k • written 8.7 years ago by ★ 1.5k
2
votes
2
replies
1.5k
views
Creating a Biostrings PDict object from amino-acid sequences
biostrings pdict
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 110
1
vote
2
replies
2.0k
views
Error in Biostrings with Fastafiles using the carriage return <cr>
biostrings software error bug
updated 8.7 years ago by 16k • written 8.8 years ago by • 0
2
votes
4
replies
1.9k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ★ 1.5k
1
vote
2
replies
3.8k
views
Perform a function on several FASTA files R (Biostrings) Error in Call2(new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings")
biostrings fasta R Call2
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
1
vote
2
replies
3.1k
views
Wrong protein sequence fetched with R's Biostrings readDNAStringSet function
biostrings fasta protein
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
0
votes
0
replies
1.6k
views
Using readAAMultipleAlignment to parse CMFinder Stockholm format alignments
biostrings stockholm msa cmfinder
8.8 years ago Keith Hughitt ▴ 180
5
votes
20
replies
4.5k
views
matching of AAStringSet vs. another AAStringSet
biostrings AAStringset
8.9 years ago tobias.kockmann ▴ 20
1
vote
3
replies
1.2k
views
Match Pattern Vector to Subject Vector
Biostings Biostrings
updated 8.9 years ago by 25k • written 8.9 years ago by ★ 1.6k
0
votes
0
replies
957
views
Biostrings readAAMultipleAlignment() does not handle valid Stockholm format files
biostrings
8.9 years ago david.huen • 0
0
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1
reply
1.5k
views
Return features from a single strand using vmatchPattern
biostrings genomicranges
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 70
0
votes
6
replies
2.4k
views
Gviz/Biostrings memory issue?
gviz biostrings
8.9 years ago stianlagstad ▴ 90
6
votes
6
replies
3.0k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges biostrings bsapply BSgenome
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 70
0
votes
0
replies
821
views
consensusString fails for AAMultipleAlignment object
biostrings
8.9 years ago Diego Diez ▴ 760
0
votes
1
reply
1.7k
views
PWM with columns that add up to 1
biostrings seqlogo pwm
updated 9.0 years ago by 700 • written 9.0 years ago by • 0
0
votes
0
replies
1.5k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings alignment
9.0 years ago map2085 ▴ 40
0
votes
5
replies
1.9k
views
Splitting a fasta file based on specific Amino acid for plotting
iranges biostrings fasta protein readaastringset
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ★ 1.5k
0
votes
1
reply
1.4k
views
Identify in tandem repeats with Bioconductor
biostrings
updated 9.1 years ago by 16k • written 9.2 years ago by ▴ 40
0
votes
2
replies
6.1k
views
Possible bug in Biostrings::readAAStringSet
bug biostrings readAAStringSet
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by • 0
0
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0
replies
1.1k
views
maxScore calculation for 'log2probratio' and 'prob' type PWMs
biostrings pwm
9.1 years ago Stefanie Tauber ▴ 40
0
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0
replies
1.1k
views
After mapping one Sanger sequence read (about 900bp) to hg19 using blastn, How can I get variants presented as reference-based position and base ch…
Biostrings blast variantannotation
9.2 years ago li lilingdu ▴ 450
4
votes
7
replies
2.0k
views
Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
Biostrings
9.3 years ago • updated 9.2 years ago matt.chambers42 ▴ 10
0
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4
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1.8k
views
BSgenome.Osativa.MSU.MSU7 Oryza sativa
bsgenome biostrings
9.4 years ago Didi ▴ 10
0
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3
replies
1.6k
views
matchPWM on DNAStringSet rather than just one sequence?
biostrings
9.4 years ago Jake ▴ 90
6
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3
replies
3.4k
views
how does coverage() works
biostrings coverage rle iranges
9.4 years ago likeeatingpizza ▴ 10
0
votes
3
replies
6.5k
views
Biostrings character vector conversion
biostrings
9.4 years ago ribioinfo ▴ 100
2
votes
1
reply
1.4k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 40
0
votes
5
replies
1.8k
views
Error Raised When Trying To Use pileup()
hilbertvis rsamtools shortread biostrings
updated 9.4 years ago by 25k • written 9.4 years ago by • 0
4
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5
replies
1.7k
views
XStringSet operations discard names - how to address?
biostrings
updated 9.4 years ago by 16k • written 9.4 years ago by • 0
3
votes
3
replies
2.3k
views
pairwiseAlignments coordinate mapping?
biostrings pairwisealignment
updated 5 months ago by ▴ 20 • written 9.4 years ago by ★ 13k
0
votes
1
reply
950
views
genome searching with Biostrings and the BSgenome data packages
biostrings
updated 9.5 years ago by 25k • written 9.5 years ago by • 0
2
votes
1
reply
1.4k
views
Error in score() function on pairwiseAlignment()
biostrings pairwisealignment
updated 9.5 years ago by 4.2k • written 9.5 years ago by • 0
292 results • Page 3 of 6
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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