Showing : SNPs • reset
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How to extract genomic positions of SNPs using snp-sites or using any R package?
SNPs
2.8 years ago pltbiotech_tkarthi • 0
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584
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vcf to venn diagram
snps vcf venn diagram ggplot2
3.1 years ago mictadlo • 0
0
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6
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635
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Physical position to gene positions
bioconductor molecular biology snps
updated 3.1 years ago by 58k • written 3.1 years ago by • 0
2
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5
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1.3k
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Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR vcf snps motif analysis
updated 3.6 years ago by ★ 6.7k • written 3.6 years ago by ▴ 780
3
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4
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816
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No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 4.6 years ago by ★ 6.7k • written 4.6 years ago by • 0
1
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1
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1.4k
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Any tool to calculate Fst on haploid data?
snps VCF
4.9 years ago rkdonthu ▴ 10
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1
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976
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Extract SNPs and INDELs
hsapiens snps indels
updated 6.1 years ago by 15k • written 6.2 years ago by • 0
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1
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866
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Counting SNPs where ambiguity codes represent heterozygosity.
Biostrings SNPs alignment
updated 6.5 years ago by 15k • written 6.5 years ago by ▴ 30
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4
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1.3k
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Marking and annotating several SNPs on Ideogram track by Gviz package.
gviz ideogram snps
updated 7.0 years ago by ★ 1.6k • written 7.0 years ago by • 0
4
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3
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1.3k
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Overlap the snps
overlap snps granges iranges
updated 7.3 years ago by 11k • written 7.3 years ago by ▴ 10
10 results • Page 1 of 1
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Comment: DiffBind: Values of Called1 and Called2 do not appear to coincide with input pea by Rory Stark ★ 4.3k
Nothing too unusual, just a bug where in certain conditions the `Called` columns were being computed using the unmerged datasets. This onl…
Answer: Unusal standard deviation after rlog transformation and the homoscedasticity of by Michael Love 35k
I'm guessing this data does not conform well to the assumptions of the rlog, which are that variation is distributed a certain way from exp…
Answer: Affymetrix chip which is not listed on this webpage by James W. MacDonald 58k
You can't use the `affy` package for Clariom S arrays, but instead have to use the `oligo` package. I don't believe `affylmGUI` uses `oligo…
Comment: deseq2 + filtering low counts with noiseq function by Michael Love 35k
Nothing especially concerning about nonparametric methods in my opinion, except that with very low sample size they lose sensitivity. E.g. …
Comment: Using DiffBind blacklists and greylists with results mapped to BDGP6 by Rory Stark ★ 4.3k
I've checked in a fix that should handle this warning condition, it is active in the currently downloadable version if you do a `BiocManage…
Votes
edgeR cpm() function with and without log2
edgeR cpm() function with and without log2
A: edgeR cpm() function with and without log2
A: edgeR cpm() function with and without log2
A: How to get all possible comparisons in DiffBind
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