Showing : SNPlocs • reset
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119
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SNP locus package for mouse?
SNPlocs packFinder
updated 9 days ago by 65k • written 12 days ago by • 0
1
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3
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578
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 6 months ago by • 0
0
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1
reply
432
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Could not find XtraSNPlocs.Hsapiens.dbSNP155.GRCh37/GRCh38 packages
XtraSNPlocs SNPlocs
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 20
1
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794
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News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.0 years ago Hervé Pagès 16k
0
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649
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.0 years ago Guandong Shang ▴ 40
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1
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1.1k
views
3.7 behaviour change with snplocs snpsById?
software error snplocs gpos
updated 5.9 years ago by 16k • written 6.0 years ago by • 0
3
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4
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How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scale?
SNPlocs SNP dbsnp
7.2 years ago Ramiro Magno ▴ 100
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2
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1.6k
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injectSNPS only for common variants
snp snplocs
updated 7.5 years ago by ★ 3.3k • written 7.5 years ago by • 0
1
vote
6
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2.3k
views
Good way to get location of in-del SNPs in UCSC coordinates?
snplocs snp
9.4 years ago garrisrg ▴ 10
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2
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1.6k
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using snpid2grange() and/or rsidsToGRanges() for rsid lists with missing
SNPlocs
updated 9.5 years ago by 6.7k • written 9.5 years ago by ▴ 20
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1.5k
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minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
9.9 years ago swarmqq@gmail.com ▴ 10
0
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3
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1.9k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
updated 10.2 years ago by ▴ 20 • written 10.2 years ago by ★ 4.2k
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2
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1.5k
views
VCF as custom variant annotation database
Annotation SNPlocs Annotation SNPlocs
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by ▴ 380
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1
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1.4k
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Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 10.4 years ago by ▴ 240 • written 10.4 years ago by 16k
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1.9k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
10.4 years ago Hervé Pagès 16k
0
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0
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2.1k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
10.4 years ago Hervé Pagès 16k
0
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1
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964
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custom variant AnnotationDbi?
Annotation SNPlocs Annotation SNPlocs
updated 10.6 years ago by 6.7k • written 10.6 years ago by ▴ 380
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2
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3.6k
views
From location to get the SNP rs ID
SNP Cancer SNPlocs ASSIGN SNP Cancer SNPlocs ASSIGN
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 970
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4
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1.8k
views
IlluminaHumanMethylation450kprobe for nearest TSS calculation question
Annotation BSgenome SNPlocs BSgenome Annotation BSgenome SNPlocs BSgenome
updated 11.1 years ago by ★ 4.2k • written 11.1 years ago by ★ 13k
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3
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1.9k
views
Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package Bioconductor x
SNP SNPlocs SNP SNPlocs
updated 11.3 years ago by 16k • written 11.3 years ago by ▴ 40
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0
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963
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Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package
SNP SNPlocs SNP SNPlocs
11.3 years ago Christina Chaivorapol ▴ 40
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4
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2.0k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 100
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3
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1.4k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 100
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4
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1.6k
views
GGtools: transScores function returning cis eQTL
SNP Annotation probe SNPlocs GGtools SNP Annotation probe SNPlocs GGtools
updated 11.6 years ago by 6.7k • written 11.6 years ago by ★ 13k
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0
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1.2k
views
dbSNP strand information
SNPlocs safe SNPlocs safe
12.2 years ago Alex Gutteridge ▴ 650
0
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3
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1.5k
views
Strand information for dbSNP packages
SNPlocs safe SNPlocs safe
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 650
0
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4
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1.4k
views
Finding coding SNPs with predictCoding
SNP VariantAnnotation BSgenome SNPlocs BSgenome VariantAnnotation SNP VariantAnnotation
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 650
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1
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1.1k
views
SNPlocs package for dbSNP 135
Cancer SNPlocs Cancer SNPlocs
updated 8.7 years ago by • 0 • written 12.2 years ago by 16k
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3
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1.8k
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RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 12.2 years ago by 16k • written 12.2 years ago by ▴ 450
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1
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1.1k
views
custom SNPlocs / BSgenome package
SNP Annotation Organism Homo sapiens BSgenome SNPlocs BSgenome SNP Annotation Organism
updated 12.4 years ago by 16k • written 12.4 years ago by ▴ 100
0
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1
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1.4k
views
Does liftOver work for SNPs mapping to different chr between different builds
SNP GO Cancer SNPlocs rtracklayer SNP GO Cancer SNPlocs rtracklayer
updated 12.5 years ago by ★ 11k • written 12.5 years ago by ★ 1.0k
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6
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1.4k
views
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 12.6 years ago by 6.7k • written 12.6 years ago by ★ 4.2k
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7
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1.7k
views
Probe ID to Sequence
SNPlocs GenomicRanges SNPlocs GenomicRanges
updated 12.7 years ago by ★ 4.2k • written 12.7 years ago by ▴ 400
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2
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1.2k
views
seqnames on dbSNP object error
SNPlocs SNPlocs
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 910
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2
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1.5k
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RE : RE : maping SNPs
SNP SNPlocs TranscriptDb IRanges GenomicFeatures SNP SNPlocs TranscriptDb IRanges
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 450
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0
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1.7k
views
RE : maping SNPs; first foundation challenge offered
SNP Annotation Cancer SNPlocs TranscriptDb biomaRt GenomicFeatures SNP Annotation Cancer
13.4 years ago Vincent J. Carey, Jr. 6.7k
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2
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1.3k
views
New SNPlocs data package for Human (dbSNP BUILD 131)
Cancer BSgenome SNPlocs BSgenome Cancer BSgenome SNPlocs BSgenome
14.0 years ago Hervé Pagès 16k
0
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3
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992
views
Fwd: cannot install SNPlocs.Hsapiens.dbSNP.20090506
SNPlocs SNPlocs
updated 14.3 years ago by ▴ 70 • written 14.3 years ago by 21k
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1
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2.7k
views
How to find SNP names
SNP Homo sapiens SNPlocs SNP Homo sapiens SNPlocs
updated 14.9 years ago by 16k • written 14.9 years ago by ▴ 90
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6
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2.2k
views
dbSNP build for R package SNPlocs.Hsapiens.dbSNP.20080617
SNP Cancer SNPlocs SNP Cancer SNPlocs
updated 8.8 years ago by • 0 • written 14.9 years ago by 16k
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3
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1.0k
views
other human genomes, other SNP sets?
Sequencing BSgenome SNPlocs BSgenome Sequencing BSgenome SNPlocs BSgenome
15.2 years ago Paul Shannon ★ 1.1k
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1.4k
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About the bioconductor package SNPlocs.Hsapiens.dbSNP.20071016.
SNP Cancer SNPlocs SNP Cancer SNPlocs
15.2 years ago Hervé Pagès 16k
0
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4
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2.5k
views
how to modify a Biostrings object
SNPlocs SNPlocs
updated 15.2 years ago by 16k • written 15.2 years ago by ★ 1.1k
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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