Pinned Repositories
bazam
A read extraction and realignment tool for next generation sequencing data
bpipe
Bpipe - a tool for running and managing bioinformatics pipelines
excelcatgory
A small utility to ease making Excel files with groovy
exome_depth_pipeline
A Bpipe pipeline for easily running ExomeDepth
gatks
A scripting interface to the Genome Analysis Toolkit (GATK)
graxxia
Wrappers for doing Mathematics in Groovy
groovy-ngs-utils
A collection of utilities for working with next generation (MPS) sequencing data in Groovy
schism
Tool for identifying novel genomic breakpoints in HTS data
variant_calling_pipeline
A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL.
ximmer
Ximmer is a system for CNV calling on exome and targeted genomic sequencing
ssadedin's Repositories
ssadedin/bpipe
Bpipe - a tool for running and managing bioinformatics pipelines
ssadedin/bazam
A read extraction and realignment tool for next generation sequencing data
ssadedin/graxxia
Wrappers for doing Mathematics in Groovy
ssadedin/ximmer
Ximmer is a system for CNV calling on exome and targeted genomic sequencing
ssadedin/groovy-ngs-utils
A collection of utilities for working with next generation (MPS) sequencing data in Groovy
ssadedin/schism
Tool for identifying novel genomic breakpoints in HTS data
ssadedin/seqr
ssadedin/beakerx
Beaker Extensions for Jupyter Notebook
ssadedin/beakerx_kernel_autotranslation
A repository for BeakerX Autotranslation components.
ssadedin/beakerx_kernel_base
Base repository for BeakerX JVM based kernels
ssadedin/beakerx_kernel_groovy
ssadedin/beakerx_tabledisplay
ssadedin/beakerx_tests
ssadedin/bioinformatics-workflows
minimal example implementations for bioinformatics workflow managers
ssadedin/hail-elasticsearch-pipelines
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
ssadedin/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
ssadedin/igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
ssadedin/jahmm
A Java Hidden Markov Model library
ssadedin/jessies
Terminator, Evergreen, lwm and friends
ssadedin/jsoncodegen
Groovy based generation tasks from JSON schema
ssadedin/koada
Front end for llama2-code-instruct
ssadedin/mitoreport
Intepretation software for mitochondrial variants
ssadedin/repo_data_020322
Some evaluation data
ssadedin/rnadx
ssadedin/rnadxview
ssadedin/SavvySuite
Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
ssadedin/ssadedin.github.io
ssadedin/vrapper
Vim-like editing in Eclipse
ssadedin/warpy
A port of the core elements of the nf-core/wf-human-variation nanopore pipeline to bpipe
ssadedin/wf-human-variation