smithlabcode Goto Github PK
Name: Smith Lab
Type: Organization
Bio: A computational biology research group at USC
Location: Los Angeles, CA
Name: Smith Lab
Type: Organization
Bio: A computational biology research group at USC
Location: Los Angeles, CA
DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.
The base repo for the smithlabcode organization
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
Amordad is a database engine for high dimensional data
HTSlib wrapper (mostly for BAM/SAM) in C++.
Software tools for regulatory sequence analysis
The DME algorithm for discovering motifs that distinguish two sets of sequences.
Tools for analyzing DNA methylation data
Programs for simulating and inferring epigenome evolution.
A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
Thousands of high-quality analyzed methylomes.
A pipeline for analyzing DNA methylation data from bisulfite sequencing.
Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels
Piranha is a peak-caller for CLIP- and RIP-seq data
Software for predicting library complexity and genome coverage in high-throughput sequencing.
An R package for estimating library complexity
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
A tool for accurately detecting actively translating ORFs from Ribo-seq data
Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data
Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)
A software tool to identify dispersed epigenetic regions from ChIP-seq data
C++ code library that includes functions used in many of the Smith lab projects
Scripts and some documentation for how we did CNV analysis using SMURF-seq reads and how we generated simulated data to evaluate mapping performance.
Scripts, pipelines, summary data and figures for this project.
A collection of utility programs that might be useful to someone.
WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
Zagros is an algorithm for motif discovery in CLIP-seq data
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.