Smith Lab

A computational biology research group at USC

Los Angeles, CA

Pinned Repositories

abismal
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
Language:C++11 6 224
dnmtools
Tools for analyzing DNA methylation data
Language:C++22 6 727
falco
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
Language:HTML88 7 4910
methpipe
A pipeline for analyzing DNA methylation data from bisulfite sequencing.
Language:C++66 17 19628
piranha
Piranha is a peak-caller for CLIP- and RIP-seq data
Language:C++17 11 2016
preseq
Software for predicting library complexity and genome coverage in high-throughput sequencing.
Language:C++75 14 6615
preseqR
An R package for estimating library complexity
Language:R10 8 293
ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
Language:Python28 5 528
ribotricer-results
Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data
Language:Jupyter Notebook8 4 50
walt
WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
Language:C++16 17 298

Smith Lab's Repositories

smithlabcode/falco
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
Language:HTML88 7 4910
smithlabcode/preseq
Software for predicting library complexity and genome coverage in high-throughput sequencing.
Language:C++75 14 6615
smithlabcode/methpipe
A pipeline for analyzing DNA methylation data from bisulfite sequencing.
Language:C++66 17 19628
smithlabcode/ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
Language:Python28 5 528
smithlabcode/dnmtools
Tools for analyzing DNA methylation data
Language:C++22 6 727
smithlabcode/piranha
Piranha is a peak-caller for CLIP- and RIP-seq data
Language:C++17 11 2016
smithlabcode/walt
WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
Language:C++16 17 298
smithlabcode/abismal
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
Language:C++11 6 224
smithlabcode/preseqR
An R package for estimating library complexity
Language:R10 8 293
smithlabcode/riborex
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Language:R8 15 102
smithlabcode/ribotricer-results
Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data
Language:Jupyter Notebook8 4 50
smithlabcode/rmap
Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)
Language:C++5 9 122
smithlabcode/rseg
A software tool to identify dispersed epigenetic regions from ChIP-seq data
Language:C5 4 8
smithlabcode/smithlab_cpp
C++ code library that includes functions used in many of the Smith lab projects
Language:C++4 19 365
smithlabcode/smurfseq_scripts
Scripts and some documentation for how we did CNV analysis using SMURF-seq reads and how we generated simulated data to evaluate mapping performance.
Language:Python4 5 61
smithlabcode/amordad
Amordad is a database engine for high dimensional data
Language:C++3 7 90
smithlabcode/Epiphyte
A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.
Language:C++3 9 32
smithlabcode/radmeth
Language:C++3 15 31
smithlabcode/mlml
Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels
Language:C++2 17 12
smithlabcode/zagros
Zagros is an algorithm for motif discovery in CLIP-seq data
Language:C++2 9 11
smithlabcode/epievo
Programs for simulating and inferring epigenome evolution.
Language:C++1 5 91
smithlabcode/utils
A collection of utility programs that might be useful to someone.
Language:C++1 5 5
smithlabcode/-DEPRECATED-amrfinder
DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.
Language:C++15 11
smithlabcode/.github
The base repo for the smithlabcode organization
8 0
smithlabcode/bamxx
HTSlib wrapper (mostly for BAM/SAM) in C++.
Language:C++7 02
smithlabcode/cread
Software tools for regulatory sequence analysis
Language:C++7 0
smithlabcode/dme
The DME algorithm for discovering motifs that distinguish two sets of sequences.
Language:C++
smithlabcode/sperm-methylome-aging-wgbs
Scripts, pipelines, summary data and figures for this project.
Language:R8 0