darogan

ISoLDE

RMDetect

RMDetect is a bioinformatics tool for 3D RNA modules (e.g. G-bulged loops, C-loops, Kink-Turns, ...) detection on genomic sequences. It allows the search for known modules, analysis of search results and incorporate new modules into the model DB.

rmsd

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

sysbiol_pt3

Code for part III systems biology main project

MEA

hunspell

The most popular spellchecking library.

kmer-counter

Count kmers with a more efficient (faster) hash table

MRtree

MRtree R implementation

DMRichR

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

emase

Expectation-Maximization algorithm for Allele-Specific Expression

configs

Config files used to define parameters specific to compute environments at different Institutions

MOFA2

Multi-Omics Factor Analysis

g2gtools

Personal diploid genome creation and coordinate conversion

ASE

early version of (Pipeline for detection of differential allelic imbalance from RNA-seq)

SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

piPipes

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

FIt-SNE

Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)

Scavenger

A pipeline for recovery of unaligned reads utilising similarity with aligned reads

Drop-seq

Java tools for analyzing Drop-seq data

haplotyped-methylome

Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation

cellphonedb

infercnv

Inferring CNV from Single-Cell RNA-Seq

SAVER

Single-cell RNA-seq Gene Expression Recovery

samplot

Plot structural variant signals from many BAMs and CRAMs

pySCA

A python implementation of the Statistical Coupling Analysis (SCA)

seqtk

Toolkit for processing sequences in FASTA/Q formats

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.