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assemblertrinity

This is one Torrent Suite Software plugin for ion torrent sequencing data assembly.

bam-tricks

Tip and tricks for BAM files

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio.rnaseq

Quality control, differential gene/transcript expression and pathway analysis for bcbio RNA-seq runs

bed2wig

benchmarking-tools

brcatesing

charger

Characterization of Germline variants

cnv_gray_zone

cobrapy

COBRApy is a package for constraint-based modeling of biological networks

codon_optimization

codon_optimization_paddle

This is a trial work to codon optimization by using deep learning algorithm based on PaddlePaddle

codon_optimize.v2

covid19consensus

This plugin builds a consensus sequence of the virus present in the sample through two rounds of mapping and variant calling (only detecting mutations with allele frequency >= 51%), and masks low and no coverage positions.

datasciencecoursera

This is a demo for data science coursera

datasharing

The Leek group guide to data sharing

dgsmef

A dynamic genome-scale modelling of E.coli fermentation

feature-selector

Feature selector is a tool for dimensionality reduction of machine learning datasets

fluxshift

to identify metabolic flux shifting significantly

gatk3_indelrealign_scatter_gather

genomeassembly

To describe a workflow for bacterial full genome finishing from PacBio RS II sequencing

giab_data_indexes

This repository contains data indexes from NIST's Genome in a Bottle project.

glibc_upgrade

Just record the installing process of glibc_2.23

innovation-impact-pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

intervar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline

ion-meta

A workflow using snakemake to analyze ion torrent based metagenomics data

machinelearning

meta16s

This is developed for analyzing 16S metagenomics data using fusion primer amplification method on Torrent Suite Software System

mutscan

Detect and visualize target mutations by scanning FastQ files directly

note

记录自己写的工具和学习笔记