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Calculate heterozygosity for each SNPs in the bim file.

snp-chip snp written 2.2 years ago by mostafarafiepour • 110

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PennCNV-Affy cluster generation for chrX/chrY in gender-specific cancer types

snp-chip affy6.0 copynumber genotype written 5.5 years ago by Charles Warden ♦ 8.0k • updated 4.7 years ago by Biostar ♦♦ 20

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Recent Replies

C: Gene expression heatmap following pseudotime analysis by Vitis • 2.4k
It's a brilliant solution! So it basically smooths the expression across features, then sorts the...
A: Error on Linear regression bulkRNAseq by rpolicastro ♦ 3.9k
prova$sex <- factor(prova$treatment, levels=c("F","M")) should be prova$sex <- ...
A: from phased SNPs to haplotype blocks (or phase sets) by Peter Chung • 130
maybe HAPCUT2 ? ./build/HAPCUT2 --fragments fragment_file --VCF variants.vcf --output haplotype_...
C: Annotating reads with the name of the feature to which they map by lech.kaczmarczyk • 0
Thanks a lot for clarification @A. Dominguez!
C: PCA plotting using DESEq2 pipeline by GenoMax ♦ 96k
This comment belongs under @ATpoint's comment in answer below. Please don't use `SUBMIT ANSWER` ...
A: PCA plotting using DESEq2 pipeline by aranyak111 • 0
Using this option I found the following results. PC1 PC2 group condition ...
C: How to interpret the gene level copy number file generated by ASCAT2 on GDC? by Kevin Blighe ♦ 71k
I have made an attempted answer, here: https://www.biostars.org/p/494728/#494755
C: BWA_MEM error "cannot find file.fa.pac" but input is file.fa by GenoMax ♦ 96k
Do you have read/write permissions to the following location? /paedyl01/disk1/yangyxt/simula...
A: Understanding TCGA's ASCAT copy number data by Kevin Blighe ♦ 71k
Dia duit, unfortunately, like many large projects, the TCGA Consortium has always struggled to ma...
A: BWA_MEM error "cannot find file.fa.pac" but input is file.fa by u3005579 • 0
I've recently suffered a lot from indexing a customized human genome (mask certain regions). I fo...
C: Confusion of the input format for DESeq2 and EdgeR for bulk- and scRNA-seq by rpolicastro ♦ 3.9k
The [tximport](https://www.bioconductor.org/packages/release/bioc/html/tximport.html) library wil...
A: Gene expression heatmap following pseudotime analysis by rpolicastro ♦ 3.9k
Generating some example data. library("tidyverse") dat <- map( set_names(seq_l...

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