Showing : Biostrings • reset
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Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
11.9 years ago Hervé Pagès 16k
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BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
11.9 years ago Hervé Pagès 16k
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How to save the result from calling matchPWM?
Biostrings Biostrings
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 200
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how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.0 years ago by ★ 11k • written 12.0 years ago by 16k
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RNAseq in silico simulator
RNASeq Biostrings RNASeq Biostrings
12.0 years ago Dave Gerrard ▴ 40
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A question when using Biostrings
Cancer Biostrings Cancer Biostrings
12.0 years ago Hervé Pagès 16k
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2
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1.4k
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Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment Cancer Biostrings IRanges Alignment Cancer Biostrings IRanges
updated 12.1 years ago by ▴ 30 • written 12.1 years ago by 16k
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Course: Understanding R / Bioconductor, Sept 30-Oct 1, Seattle
Cancer Biostrings biomaRt IRanges GenomicRanges Cancer Biostrings biomaRt IRanges
12.2 years ago Martin Morgan 25k
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14
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4.5k
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Trimming of partial adaptor sequences
Sequencing Cancer Biostrings Sequencing Cancer Biostrings
12.3 years ago Taylor, Sean D ▴ 250
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1.4k
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stringDist ?
Cancer Biostrings Cancer Biostrings
12.6 years ago Hervé Pagès 16k
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815
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Expected value of finding a sequence
Biostrings IRanges Biostrings IRanges
12.6 years ago Tim Smith ★ 1.1k
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Biostrings
GO Cancer Biostrings cycle GO Cancer Biostrings cycle
12.7 years ago Hervé Pagès 16k
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reading fasta file into R
Biostrings Biostrings
updated 13.3 years ago by 6.7k • written 13.3 years ago by ★ 13k
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6
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2.5k
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Biostring: print sequence alignment to file
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.3 years ago by ▴ 100 • written 13.3 years ago by 16k
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Biostring: print sequence alignment to file
Sequencing Alignment Cancer Biostrings Sequencing Alignment Cancer Biostrings
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 100
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pairwiseAlignment of PDB files to canonical protein structure
Alignment Biostrings PROcess Alignment Biostrings PROcess
13.4 years ago Gregory Ryslik ▴ 10
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13
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2.6k
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PWMscoreStartingAt and ambiguous subject seqs
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 740
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2
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Calculating alignment scores from aligned sequences
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ★ 13k
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11
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Biostring: print sequence alignment to file
Alignment Biostrings Alignment Biostrings
updated 13.5 years ago by ★ 1.7k • written 13.5 years ago by ▴ 100
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Non ambiguous DNA runs
Biostrings Biostrings
updated 13.5 years ago by ▴ 590 • written 13.5 years ago by ▴ 390
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896
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oligonucleotideTransitions from Biostrings package
Cancer Biostrings Cancer Biostrings
13.6 years ago Hervé Pagès 16k
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776
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oligonucleotideTransitions from Biostrings package
Biostrings Biostrings
13.6 years ago Muino, Jose ▴ 10
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1.5k
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
13.6 years ago Matthew Young ▴ 50
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings BSgenome rtracklayer goseq GO
13.7 years ago Alicia Oshlack ▴ 100
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer BSgenome Biostrings BSgenome rtracklayer GenomicFeatures goseq GO
13.7 years ago Hervé Pagès 16k
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2
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1.1k
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OS X 10.7.x "Lion"
Biostrings Biostrings
updated 13.7 years ago by ★ 1.2k • written 13.7 years ago by ▴ 70
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Biostrings - pairwiseAlignment trimmed pattern returned
Alignment Biostrings Alignment Biostrings
updated 13.7 years ago by ★ 6.8k • written 13.7 years ago by ▴ 210
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Fwd: the diffrent alignment result between pairwiseAlignment() in Biostrings package and EBI-webserver
Alignment Cancer Biostrings Alignment Cancer Biostrings
updated 13.8 years ago by ★ 6.8k • written 13.8 years ago by ▴ 50
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the diffrent alignment result between pairwiseAlignment() in Biostrings package and EBI-webserver
Alignment Biostrings Alignment Biostrings
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 50
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821
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biostrints translate() ambiguities?
Biostrings Biostrings
13.9 years ago Guest User ★ 13k
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1.7k
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RE : RE : rsamtools installation
Cancer Biostrings IRanges Rsamtools BiocInstaller Cancer Biostrings IRanges Rsamtools
updated 13.9 years ago by ▴ 140 • written 13.9 years ago by 25k
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[Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 14.1 years ago by ★ 11k • written 14.1 years ago by 16k
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the same problem happened
Biostrings Biostrings
updated 14.1 years ago by 21k • written 14.1 years ago by ★ 2.0k
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3
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1.4k
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[Bioc-sig-seq] first remove low quality or adaptor
Cancer Biostrings convert Cancer Biostrings convert
updated 14.1 years ago by ★ 2.0k • written 14.1 years ago by 16k
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6
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SNPcounts error in SNPlocs.Hsapiens.dbSNP.20110815_0.99.3 (i.e., my attempt to update SNPlocs to dbSNP build 134)
Regression SNPlocs Biostrings Regression SNPlocs Biostrings
updated 14.1 years ago by 6.7k • written 14.1 years ago by ★ 4.2k
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3
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Problem with Biostrings
Biostrings Biostrings
14.2 years ago Guido Leoni ▴ 200
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To find rsIDs
Biostrings Biostrings
updated 14.2 years ago by 6.7k • written 14.2 years ago by ▴ 400
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align microRNA with custom mRNA sequences
Alignment Cancer Biostrings microRNA Alignment Cancer Biostrings microRNA
14.2 years ago Hervé Pagès 16k
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2
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2.1k
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using and combining of "subseq"
Biostrings Biostrings
updated 14.4 years ago by ▴ 590 • written 14.4 years ago by ▴ 10
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825
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alternative to matchprobes
matchprobes Biostrings matchprobes Biostrings
updated 14.5 years ago by 16k • written 14.5 years ago by ▴ 10
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[Course] CSAMA 2011: Computational Statistics for Genome Biology (Ninth Edition)
Sequencing Microarray Alignment Annotation Clustering Cancer Biostrings AnnotationDbi
14.6 years ago stefano iacus ▴ 430
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RE : Question about translate funciton in Biostrings package
Organism Biostrings Organism Biostrings
14.6 years ago li lilingdu ▴ 450
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2.3k
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Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings GenomicFeatures Biostrings GenomicFeatures
updated 14.6 years ago by ★ 11k • written 14.7 years ago by 16k
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1
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1.7k
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Help about 'pairwiseAlignment' in Biostrings package
Alignment Biostrings Alignment Biostrings
updated 14.6 years ago by 16k • written 14.6 years ago by ▴ 450
0
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9
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2.4k
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Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.7 years ago by 21k • written 14.7 years ago by 16k
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2
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1.4k
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How Does one subset a XStringView or PDict object?
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 14.7 years ago by 25k • written 14.7 years ago by ▴ 410
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13
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3.4k
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forge BSgenome data package
BSgenome Biostrings BSgenome BSgenome Biostrings BSgenome
updated 14.8 years ago by 16k • written 14.8 years ago by ▴ 330
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2
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1.2k
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rtracklayer issues with other packages?
GO Cancer BSgenome graph Biostrings GOstats BSgenome rtracklayer GO Cancer BSgenome
updated 14.9 years ago by ★ 11k • written 14.9 years ago by ▴ 200
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1
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896
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Biostrings pdf, missing? 'Efficient genome searching with Biostrings and the BSgenome data package'
Preprocessing BSgenome Biostrings BSgenome Preprocessing BSgenome Biostrings BSgenome
updated 15.1 years ago by ★ 8.2k • written 15.1 years ago by ★ 1.1k
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2
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Difficulties updating Biostrings on Ubuntu
Biostrings Biostrings
updated 15.2 years ago by ★ 4.3k • written 15.2 years ago by ▴ 210
292 results • Page 5 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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