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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation Annotation GenomicRanges VariantAnnotation GenomicAlignments Annotation
9.8 years ago Valerie Obenchain ★ 6.8k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation GenomicRanges VariantAnnotation VariantAnnotation GenomicRanges
updated 9.8 years ago by ★ 3.3k • written 9.8 years ago by ★ 6.8k
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10
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2.8k
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GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.9 years ago by ▴ 320 • written 9.9 years ago by ★ 6.8k
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552
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Bioconductor newsletter - July 2014
Cancer Cancer
9.9 years ago Valerie Obenchain ★ 6.8k
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4
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1.5k
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GenomicAlignments and QNAME collision
RNASeq Cancer convert Rsamtools GenomicAlignments RNASeq Cancer convert Rsamtools
updated 9.9 years ago by ▴ 90 • written 9.9 years ago by ★ 6.8k
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2
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687
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Bioconductor newsletter: April 2014
Cancer Cancer
updated 10.1 years ago by ★ 1.6k • written 10.1 years ago by ★ 6.8k
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0
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1.1k
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ensemblVEP, variant_effect_predictor versions and release schedule
Cancer MLInterfaces bridge ensemblVEP AnnotationHub Cancer MLInterfaces bridge ensemblVEP
10.4 years ago Valerie Obenchain ★ 6.8k
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0
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1.3k
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zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
10.5 years ago Valerie Obenchain ★ 6.8k
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2
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1.1k
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readVcf fails when ALT field contains breakends and no symbolic allele
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 10.5 years ago by ▴ 40 • written 10.5 years ago by ★ 6.8k
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1
reply
834
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stranded intronic variants with VariantAnnotation::locateVariants()
Annotation Annotation
updated 10.5 years ago by ★ 3.3k • written 10.5 years ago by ★ 6.8k
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0
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695
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VariantAnnotation: Specifying 'seqinfo' at import with 'readVcf'
GenomicRanges GenomicRanges
10.6 years ago Valerie Obenchain ★ 6.8k
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2
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848
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using a gtf file to map reads
GO GenomicFeatures DEXSeq GO GenomicFeatures DEXSeq
updated 10.9 years ago by ★ 1.9k • written 10.9 years ago by ★ 6.8k
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453
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summarizeOverlaps: ambiguous method dispatch
GO GO
10.9 years ago Valerie Obenchain ★ 6.8k
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0
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978
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[devteam-bioc] sort error in GRange
rtracklayer GenomicRanges rtracklayer GenomicRanges
11.0 years ago Valerie Obenchain ★ 6.8k
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1
reply
1.2k
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summarizeOverlaps mode ignoring inter feature overlaps
GenomicRanges Rsamtools GenomicRanges Rsamtools
updated 11.0 years ago by ★ 1.7k • written 11.0 years ago by ★ 6.8k
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0
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1.0k
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Subsetting vcf file by subject
VariantAnnotation Annotation cycle VariantAnnotation VariantAnnotation Annotation cycle
11.1 years ago Valerie Obenchain ★ 6.8k
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4
replies
5.6k
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merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.3 years ago by ★ 6.8k
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0
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415
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ExpressionSet Object
11.2 years ago Valerie Obenchain ★ 6.8k
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1
reply
599
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Why does a call to "unique" removes a DNAStringSet names?
updated 11.5 years ago by 16k • written 11.5 years ago by ★ 6.8k
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0
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1.4k
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Rle factors, table and empty levels
IRanges IRanges
11.5 years ago Valerie Obenchain ★ 6.8k
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1
reply
2.5k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 11.7 years ago by ★ 1.2k • written 11.7 years ago by ★ 6.8k
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0
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1.4k
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GenomicRanges: nearest() for GRanges not returning overlaps
IRanges GenomicRanges IRanges GenomicRanges
11.7 years ago Valerie Obenchain ★ 6.8k
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0
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722
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Bioc2012 : July 24-25
Microarray Microarray
11.9 years ago Valerie Obenchain ★ 6.8k
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0
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519
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BioC2012 deadlines
11.9 years ago Valerie Obenchain ★ 6.8k
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0
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725
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BioC 2012
12.0 years ago Valerie Obenchain ★ 6.8k
0
votes
1
reply
922
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Finding coding SNPs with predictCoding
SNP Annotation BSgenome BSgenome GenomicFeatures cycle genomes SNP Annotation BSgenome
updated 12.0 years ago by ★ 1.7k • written 12.0 years ago by ★ 6.8k
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1
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1.1k
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Question regarding COA plot generated by made4 package
made4 made4
updated 12.0 years ago by ▴ 510 • written 12.0 years ago by ★ 6.8k
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7
replies
1.2k
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distanceToNearest for GRanges?
Cancer GenomicRanges Cancer GenomicRanges
updated 12.1 years ago by ▴ 420 • written 12.1 years ago by ★ 6.8k
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2
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1.2k
views
Finding coding SNPs with predictCoding
SNP Annotation BSgenome ctc BSgenome cycle genomes SNP Annotation BSgenome ctc BSgenome
updated 12.1 years ago by ★ 1.7k • written 12.1 years ago by ★ 6.8k
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5
replies
1.4k
views
Finding coding SNPs with predictCoding
SNP ctc SNP ctc
updated 12.2 years ago by ★ 1.7k • written 12.2 years ago by ★ 6.8k
0
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1
reply
796
views
countOverlaps within Mode Counting
Cancer Cancer
updated 12.2 years ago by ★ 1.5k • written 12.2 years ago by ★ 6.8k
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2
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1.2k
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Help With RNA-seq
Annotation Normalization Kidney edgeR baySeq Annotation Normalization Kidney edgeR baySeq
12.3 years ago Valerie Obenchain ★ 6.8k
0
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0
replies
1.2k
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[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
12.3 years ago Valerie Obenchain ★ 6.8k
0
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3
replies
2.4k
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
Microarray GO Cancer Breast gage Microarray GO Cancer Breast gage
updated 12.3 years ago by ▴ 200 • written 12.3 years ago by ★ 6.8k
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0
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800
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countGenomicOverlaps output
GenomicRanges GenomicRanges
12.6 years ago Valerie Obenchain ★ 6.8k
0
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0
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953
views
rsamtools scanBcf segfault
VariantAnnotation Rsamtools VariantAnnotation VariantAnnotation Rsamtools VariantAnnotation
12.7 years ago Valerie Obenchain ★ 6.8k
0
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0
replies
1.1k
views
PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
12.8 years ago Valerie Obenchain ★ 6.8k
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0
replies
462
views
BioC2011 - lab preparation
12.8 years ago Valerie Obenchain ★ 6.8k
0
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0
replies
597
views
BioC2011 - lab sign up
12.8 years ago Valerie Obenchain ★ 6.8k
0
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0
replies
661
views
BioC2011 - registration reminder
12.9 years ago Valerie Obenchain ★ 6.8k
0
votes
1
reply
1.9k
views
maSigPro and "subscript out of bounds"
Normalization Regression maSigPro Normalization Regression maSigPro
updated 12.9 years ago by ▴ 240 • written 12.9 years ago by ★ 6.8k
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0
replies
596
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call for BioC2011 posters
13.0 years ago Valerie Obenchain ★ 6.8k
0
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0
replies
1.2k
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[maSigPro] Splitting data - how?
maSigPro maSigPro
13.0 years ago Valerie Obenchain ★ 6.8k
0
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0
replies
1.0k
views
Bioconductor
cdf affy affyPara cdf affy affyPara
13.6 years ago Valerie Obenchain ★ 6.8k
44 results • Page 1 of 1
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