zzygyx9119 Goto Github PK

oneliners

Useful bash one-liners for bioinformatics.

open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

paired-tag

Analysis of Paired-Tag datasets

pancanatlasgermline

panelcn.mops

CNV detection tool for targeted NGS panel data

parallel_ml_tutorial

Tutorial on scikit-learn and IPython for parallel machine learning

parapindel

A parallel version of Pindel to accelerate structural variation detection

parfit

A package for parallelizing the fit and flexibly scoring of sklearn machine learning models, with visualization routines.

patterns

A curated collection of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html

pb-human-wgs-workflow-snakemake

Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads

pbpython

Code, Notebooks and Examples from Practical Business Python

pdl-ml

machine learning example code in PDL (Perl Data Language)

perl-for-bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics

pg2dm-python

ph525x

ph525x. functions only, no data

pharmcat

The Pharmacogenomic Clinical Annotation Tool - take genome data, make haplotype calls, get CPIC annotations.

phaser

phasing and Allele Specific Expression from RNA-seq

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

plasmaseq

Analyze CNVs of ctDNA

plastid

Position-wise analysis of sequencing and genomics data

platypus

Platypus Variant Caller

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.

portal-teachingdb

A simplified version of the Portal Project database designed for teaching

precisionhealthvirtualenvironment

This is a virtual environment which contains databases, software, workflows, and workshops for Precision Health Data Analysis.

pretty-vim-python

Textmate like highlighting and syntax for vi in python.

primer-lint

Primer analysis tool for the hiplex protocol - http://kiwwa.github.io/primer-lint

primerdesignpcr

Python scripts to design and check primer stats for PCR

pro-machine-learning-algorithms

Source Code for 'Pro Machine Learning Algorithms' by Kishore Ayyadevara