misshie

ngsdat2

NGS Data Analysis Textbook Version 2 (Disease Genome Analysis)

bioruby-ucsc-api

Ruby UCSC API: An API for the UCSC Genome Database

Workflows

Pwrake for bioinfomatics workflows using GATK and Dindel

bioruby-genomic-interval

a BioRuby plugin: handling genomic interavals and overlaps

hgvd2annovar

Convert a HGVD table file to an ANNOVAR generic DB file

RareDiseaseInformatics

https://misshie.github.io/rdinfo2020/

bio-virtuoso

A Doker container for a wrapper server of the Virtuoso database engine and data-containers bioinfomatics databases

bioruby-dbsnp

Utilities to handle dbSNP bitfield information

docker-ucsc-blat

Dockerfiles for UCSC BLAT servers with hg19 and hg38 reference genomes

UCSC2VCF

Convert UCSC dbSNP to VCF files

bioinformatics

Tools for bioinformatics

UCSCBin

Utilities for UCSC Bioinformatics Genome Browser ( http://genome.ucsc.edu ) including calculation of a BIN index from a genomic interval to speed-up SQL queries, and conversion between 1-based full-closed (for humans) and 0-based half-open (for machienes) intervals

avsummary

GATK & ANNOVAR workflow tool

bioruby-rakehelper

A BioRuby plugin: helper methods simplifying rakefiles

biogems.info

Tools for keeping track of biogems through http://biogems.info/

bioruby-samtools

Porting of samtools-ruby to BioRuby. Binder of samtools for ruby, on the top of FFI -from original project-

HPViewer

novo-tag-adjust

Convert "A SAM file generated by Novoalign using reference sequences containing ambiguous nucleotides" to "A SAM file with corrected NM tags ignoring ambifuous nucleotides""

PanelDoC

A targeted-sequencing CNV Calling Script written in R

tandem-genotypes

virtuoso-go-hpo

A dockerfile to invoke the Virtuoso database preloaded GO, HPO and HPO annotations

xCAT_ja

xCAT information in Japanese