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5years

advancedjavaproject

PDB Sequence Reader, 2D/3D Structure Viewer

aracne-cyni

aRACNE Cytoscape App

automation-report

Automation report是一款可以解决很多行业领域中设涉及到报告生成的需求，本项目最开始的初衷是为公司内部简化人工流程的一个环节，主要实现目的是将实验室检测得出的下机数据结果与对应的报告模版批量结合生成报告(.pdf)。

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

bioinformatics-cook

perl scripts for bioinformatics analysis

biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java framework for processing biological data.

biophysics

BioPhysics Assignment: Parse the pdb file to get the coordinates of each atom at a given lattice point of a protein and then using its symmetric and translation matrices, calculate the coordinates of all the vertices in its crystal structure.

biopieces

Biopieces is a bioinformatic framework of tools easily used and easily created.

bioscript-1

breakdancer

SV detection from paired end reads mapping

bridgedb.cytoscape

BridgeDb App for Cytoscape 3

bsvf

Bisulfite Sequencing Virus integration Finder

capsim

chinese-copywriting-guidelines

Chinese copywriting guidelines for better written communication／中文文案排版指北

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

cnvkit

Copy number variant detection from targeted DNA sequencing

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

comet_original

The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest. coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation). The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on the Encode project. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data, e.g. gene expression array data.

comogphogextractor

This project is usedto extract comogphog feature from pdb style files for our bioinformatics research project on fast and efficient protein tertiary structure retrieval algorithms. Here we used some code from an open source image retrieval library "lire" (http://www.semanticmetadata.net/lire/) and modified some of those code as per our project requirements. This extracted comogphog feature is used to compare protein tertiary structure for our academic research on fast and efficient protein tertiary structure retrieval.

covgen

Creates a target specific exome_full192.coverage.txt file required by MutSig

cpghmmexample

An example of a simple HMM to find CpG sites

crisporpaper

Code for the CRISPOR article, all data and code to create figures and analysis

crisporwebsite

All source code of the crispor.org website

crispr-dav

CRISPR NGS data analysis and visualization pipeline

cypath2

Cytoscape 3 app that connects to PC2 (cpath2) and imports BioPAX sub-networks into Cytoscape 3 for analysis.

cytoscape-api

Cytoscape 3 API bundles.

cytoscape-app-samples

Cytoscape 3 sample code for App developers.

cytoscape-impl

Cytoscape 3 implementation bundles.

data-science-from-scratch

code for Data Science From Scratch book