smithlabcode/methpipe

This repository has been archived on 17/Oct/2022
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Created over 10 years ago
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smithlabcode/methpipe

smithlabcode

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A pipeline for analyzing DNA methylation data from bisulfite sequencing.

falco

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

preseq

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

ribotricer

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

dnmtools

Tools for analyzing DNA methylation data

piranha

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

walt

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

preseqR

An R package for estimating library complexity

abismal

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

riborex

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

ribotricer-results

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

Jupyter Notebook

rmap

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

rseg

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

smithlab_cpp

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

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.

amordad

Amordad is a database engine for high dimensional data

radmeth

Epiphyte

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

zagros

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

mlml

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

epievo

Programs for simulating and inferring epigenome evolution.

utils

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