Showing : SNPlocs • reset
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SNP locus package for mouse?
SNPlocs packFinder
updated 12 months ago by 68k • written 12 months ago by • 0
1
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3
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1.1k
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 18 months ago by • 0
0
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1
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746
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Could not find XtraSNPlocs.Hsapiens.dbSNP155.GRCh37/GRCh38 packages
XtraSNPlocs SNPlocs
updated 2.3 years ago by ★ 4.8k • written 2.3 years ago by ▴ 20
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News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
3.0 years ago Hervé Pagès 16k
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880
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
4.0 years ago Guandong Shang ▴ 40
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1
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1.4k
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3.7 behaviour change with snplocs snpsById?
software error snplocs gpos
updated 6.9 years ago by 16k • written 7.0 years ago by • 0
3
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How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scale?
SNPlocs SNP dbsnp
8.2 years ago Ramiro Magno ▴ 100
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injectSNPS only for common variants
snp snplocs
updated 8.5 years ago by ★ 3.4k • written 8.5 years ago by • 0
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1.3k
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SNPlocs package for dbSNP 135
Cancer SNPlocs Cancer SNPlocs
updated 9.7 years ago by • 0 • written 13.2 years ago by 16k
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6
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2.7k
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dbSNP build for R package SNPlocs.Hsapiens.dbSNP.20080617
SNP Cancer SNPlocs SNP Cancer SNPlocs
updated 9.8 years ago by • 0 • written 15.9 years ago by 16k
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2.7k
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Good way to get location of in-del SNPs in UCSC coordinates?
snplocs snp
10.4 years ago garrisrg ▴ 10
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2.0k
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using snpid2grange() and/or rsidsToGRanges() for rsid lists with missing
SNPlocs
updated 10.5 years ago by 6.7k • written 10.5 years ago by ▴ 20
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minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.9 years ago swarmqq@gmail.com ▴ 10
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3
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2.2k
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minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
updated 11.2 years ago by ▴ 20 • written 11.2 years ago by ★ 4.2k
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1.9k
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VCF as custom variant annotation database
Annotation SNPlocs Annotation SNPlocs
updated 11.3 years ago by ★ 6.8k • written 11.3 years ago by ▴ 380
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2.9k
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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 11.4 years ago by ▴ 280 • written 11.4 years ago by 16k
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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
11.4 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
11.4 years ago Hervé Pagès 16k
0
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1.2k
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custom variant AnnotationDbi?
Annotation SNPlocs Annotation SNPlocs
updated 11.6 years ago by 6.7k • written 11.6 years ago by ▴ 380
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4.2k
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From location to get the SNP rs ID
SNP Cancer SNPlocs ASSIGN SNP Cancer SNPlocs ASSIGN
updated 11.9 years ago by 16k • written 11.9 years ago by ▴ 970
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4
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2.0k
views
IlluminaHumanMethylation450kprobe for nearest TSS calculation question
Annotation BSgenome SNPlocs BSgenome Annotation BSgenome SNPlocs BSgenome
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ★ 13k
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2.1k
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Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package Bioconductor x
SNP SNPlocs SNP SNPlocs
updated 12.3 years ago by 16k • written 12.3 years ago by ▴ 40
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1.1k
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Problem locating SNP by rsID for SNPlocs.Hsapiens.dbSNP.20120608 package
SNP SNPlocs SNP SNPlocs
12.3 years ago Christina Chaivorapol ▴ 40
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4
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2.4k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 12.6 years ago by 16k • written 12.6 years ago by ▴ 100
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1.6k
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predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 12.6 years ago by 16k • written 12.6 years ago by ▴ 100
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4
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1.9k
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GGtools: transScores function returning cis eQTL
SNP Annotation probe SNPlocs GGtools SNP Annotation probe SNPlocs GGtools
updated 12.6 years ago by 6.7k • written 12.6 years ago by ★ 13k
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dbSNP strand information
SNPlocs safe SNPlocs safe
13.2 years ago Alex Gutteridge ▴ 650
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3
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1.7k
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Strand information for dbSNP packages
SNPlocs safe SNPlocs safe
updated 13.2 years ago by ★ 6.8k • written 13.2 years ago by ▴ 650
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1.7k
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Finding coding SNPs with predictCoding
SNP VariantAnnotation BSgenome SNPlocs BSgenome VariantAnnotation SNP VariantAnnotation
updated 13.2 years ago by ★ 6.8k • written 13.2 years ago by ▴ 650
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RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 13.2 years ago by 16k • written 13.2 years ago by ▴ 450
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1.3k
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custom SNPlocs / BSgenome package
SNP Annotation Organism Homo sapiens BSgenome SNPlocs BSgenome SNP Annotation Organism
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 100
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1.7k
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Does liftOver work for SNPs mapping to different chr between different builds
SNP GO Cancer SNPlocs rtracklayer SNP GO Cancer SNPlocs rtracklayer
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ★ 1.0k
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1.8k
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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 13.6 years ago by 6.7k • written 13.6 years ago by ★ 4.2k
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Probe ID to Sequence
SNPlocs GenomicRanges SNPlocs GenomicRanges
updated 13.7 years ago by ★ 4.2k • written 13.7 years ago by ▴ 400
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seqnames on dbSNP object error
SNPlocs SNPlocs
updated 14.1 years ago by 16k • written 14.1 years ago by ▴ 910
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1.8k
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RE : RE : maping SNPs
SNP SNPlocs TranscriptDb IRanges GenomicFeatures SNP SNPlocs TranscriptDb IRanges
updated 14.3 years ago by ★ 6.8k • written 14.3 years ago by ▴ 450
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1.8k
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RE : maping SNPs; first foundation challenge offered
SNP Annotation Cancer SNPlocs TranscriptDb biomaRt GenomicFeatures SNP Annotation Cancer
14.4 years ago Vincent J. Carey, Jr. 6.7k
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New SNPlocs data package for Human (dbSNP BUILD 131)
Cancer BSgenome SNPlocs BSgenome Cancer BSgenome SNPlocs BSgenome
15.0 years ago Hervé Pagès 16k
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3
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1.2k
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Fwd: cannot install SNPlocs.Hsapiens.dbSNP.20090506
SNPlocs SNPlocs
updated 15.3 years ago by ▴ 70 • written 15.3 years ago by 21k
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1
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3.1k
views
How to find SNP names
SNP Homo sapiens SNPlocs SNP Homo sapiens SNPlocs
updated 15.9 years ago by 16k • written 15.9 years ago by ▴ 90
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1.2k
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other human genomes, other SNP sets?
Sequencing BSgenome SNPlocs BSgenome Sequencing BSgenome SNPlocs BSgenome
16.2 years ago Paul Shannon ★ 1.1k
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1.6k
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About the bioconductor package SNPlocs.Hsapiens.dbSNP.20071016.
SNP Cancer SNPlocs SNP Cancer SNPlocs
16.2 years ago Hervé Pagès 16k
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4
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2.9k
views
how to modify a Biostrings object
SNPlocs SNPlocs
updated 16.2 years ago by 16k • written 16.2 years ago by ★ 1.1k
43 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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