Smith Lab

Smith Lab's repositories

falco

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

Language:HTMLGPL-3.085 7 48

preseq

Software for predicting library complexity and genome coverage in high-throughput sequencing.

Language:C++GPL-3.073 14 66

methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

Language:C++66 17 196

ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data

Language:PythonGPL-3.027 5 50

dnmtools

Tools for analyzing DNA methylation data

Language:C++GPL-3.022 6 72

piranha

Piranha is a peak-caller for CLIP- and RIP-seq data

Language:C++17 11 19

walt

WALT is a read mapping program for bisulfite sequencing DNA methylation studies.

Language:C++GPL-3.016 17 29

abismal

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

Language:C++GPL-3.011 6 22

preseqR

An R package for estimating library complexity

Language:R10 8 29

riborex

Riborex: Fast and flexible identification of differential translation from Ribo-seq data

Language:R8 15 10

ribotricer-results

Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data

Language:Jupyter Notebook8 4 5

rmap

Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)

Language:C++5 9 12

rseg

A software tool to identify dispersed epigenetic regions from ChIP-seq data

Language:C5 4 8

smithlab_cpp

C++ code library that includes functions used in many of the Smith lab projects

Language:C++4 19 36

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:PythonGPL-3.04 5 6

amordad

Amordad is a database engine for high dimensional data

Language:C++GPL-3.03 7 9

Epiphyte

A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.

Language:C++GPL-3.03 9 3

radmeth

Language:C++GPL-3.03 15 3

mlml

Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels

Language:C++2 17 1

zagros

Zagros is an algorithm for motif discovery in CLIP-seq data

Language:C++2 9 11

epievo

Programs for simulating and inferring epigenome evolution.

Language:C++GPL-3.01 5 9

utils

A collection of utility programs that might be useful to someone.

Language:C++1 5 5

-DEPRECATED-amrfinder

DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.

Language:C++015 1

.github

The base repo for the smithlabcode organization

080

bamxx

HTSlib wrapper (mostly for BAM/SAM) in C++.

Language:C++MIT070

cread

Software tools for regulatory sequence analysis

Language:C++GPL-3.0070

dme

The DME algorithm for discovering motifs that distinguish two sets of sequences.

Language:C++000

sperm-methylome-aging-wgbs

Scripts, pipelines, summary data and figures for this project.

Language:RGPL-3.0000