Showing : snplocs • reset
3
votes
4
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1.5k
views
How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scale?
SNPlocs SNP dbsnp
7.2 years ago Ramiro Magno ▴ 100
1
vote
0
replies
808
views
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
1
vote
6
replies
2.3k
views
Good way to get location of in-del SNPs in UCSC coordinates?
snplocs snp
9.4 years ago garrisrg ▴ 10
1
vote
3
replies
591
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 6 months ago by • 0
0
votes
3
replies
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
0
votes
6
replies
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
0
votes
1
reply
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
0
votes
3
replies
998
views
Fwd: cannot install SNPlocs.Hsapiens.dbSNP.20090506
SNPlocs SNPlocs
updated 14.3 years ago by ▴ 70 • written 14.3 years ago by 21k
0
votes
2
replies
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
votes
2
replies
1.2k
views
seqnames on dbSNP object error
SNPlocs SNPlocs
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 910
0
votes
7
replies
1.7k
views
Probe ID to Sequence
SNPlocs GenomicRanges SNPlocs GenomicRanges
updated 12.8 years ago by ★ 4.2k • written 12.8 years ago by ▴ 400
0
votes
6
replies
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
0
votes
1
reply
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
0
votes
1
reply
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
votes
3
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1.8k
views
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
0
votes
1
reply
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
0
votes
4
replies
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
0
votes
3
replies
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
votes
0
replies
1.2k
views
dbSNP strand information
SNPlocs safe SNPlocs safe
12.2 years ago Alex Gutteridge ▴ 650
0
votes
4
replies
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
0
votes
3
replies
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
0
votes
4
replies
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
0
votes
0
replies
968
views
Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package
SNP SNPlocs SNP SNPlocs
11.3 years ago Christina Chaivorapol ▴ 40
0
votes
3
replies
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
0
votes
4
replies
1.8k
views
IlluminaHumanMethylation450kprobe for nearest TSS calculation question
Annotation BSgenome SNPlocs BSgenome Annotation BSgenome SNPlocs BSgenome
updated 11.2 years ago by ★ 4.2k • written 11.2 years ago by ★ 13k
0
votes
2
replies
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
0
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1
reply
1.4k
views
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
0
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0
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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
votes
1
reply
976
views
custom variant AnnotationDbi?
Annotation SNPlocs Annotation SNPlocs
updated 10.6 years ago by 6.7k • written 10.6 years ago by ▴ 380
0
votes
0
replies
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
votes
2
replies
1.6k
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
0
votes
3
replies
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 10.3 years ago by ★ 4.2k
0
votes
0
replies
1.5k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.0 years ago swarmqq@gmail.com ▴ 10
0
votes
2
replies
1.6k
views
using snpid2grange() and/or rsidsToGRanges() for rsid lists with missing
SNPlocs
updated 9.6 years ago by 6.7k • written 9.6 years ago by ▴ 20
0
votes
2
replies
1.6k
views
injectSNPS only for common variants
snp snplocs
updated 7.5 years ago by ★ 3.3k • written 7.5 years ago by • 0
0
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1
reply
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
0
votes
1
reply
438
views
Could not find XtraSNPlocs.Hsapiens.dbSNP155.GRCh37/GRCh38 packages
XtraSNPlocs SNPlocs
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 20
0
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0
replies
662
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.1 years ago Guandong Shang ▴ 40
0
votes
2
replies
1.5k
views
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
0
votes
1
reply
138
views
SNP locus package for mouse?
SNPlocs packFinder
updated 18 days ago by 65k • written 21 days ago by • 0
0
votes
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
0
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4
replies
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
0
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0
replies
1.4k
views
About the bioconductor package SNPlocs.Hsapiens.dbSNP.20071016.
SNP Cancer SNPlocs SNP Cancer SNPlocs
15.2 years ago Hervé Pagès 16k
43 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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