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Eric Edsinger's starred repositories

mojo

The Mojo Programming Language

Language:MojoNOASSERTION22390 264 1939

panel

Panel: The powerful data exploration & web app framework for Python

Language:PythonBSD-3-Clause4483 57 3481

treelib

An efficient implementation of tree data structure in python 2/3.

Language:PythonNOASSERTION802 30 130

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Language:CGPL-3.0712 20 277

cactus

Official home of genome aligner based upon notion of Cactus graphs

Language:CNOASSERTION486 21 804

Kilosort

Fast spike sorting with drift correction for up to a thousand channels

Language:PythonGPL-3.0437 29 680

MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

Language:CAP CDS210 15 70

MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies

Language:PythonMIT162 5 71

read2tree

a tool for inferring species tree from sequencing reads

Language:PythonMIT138 11 58

MotionMapper

Sample implementation of the MotionMapper behavioral analysis algorithms

Language:MATLAB76 14 2

TranscriptomeAssemblyTools

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.

Language:Python47 13 10

Inspector

A tool for evaluate long-read de novo assembly results

Language:PythonMIT39 20

goldrush

Linear-time de novo Long Read Assembler

Language:C++GPL-3.033 10 43

cellsnake

Cellsnake tool main repo

Language:PythonMIT33 2 5

Identity

Language:C++NOASSERTION32 3 23

STGRNS

Language:Jupyter Notebook24 20

ALFATClust

Biological sequence clustering tool with dynamic threshold

Language:PythonGPL-3.022 3 12

CNEFinder

CNEFinder: Finding Conserved Non-coding Elements in Genomes

Language:C++GPL-3.019 5 13

polishCLR

A nextflow pipeline for polishing CLR assemblies

Language:Nextflow16 4 30

HogProf

Phylogenetic profiling with orthology data

Language:Jupyter NotebookMIT9 7 1

SLHSD

Hybird Scaffolding Tool

Language:C++Apache-2.07 2 2

synphoni

SYNPHONI is a tool designed for reconstructing the dynamic evolution of syntenic relationships across all scales of phylogenetic distance and genome organization. It thus provides a syntenic complement not only for the last common ancestor of all sample species but for each node of interest within a user-provided cladogram (polytomies accepted). Furthermore, syntenic blocks of extant species are retrieved regardless of whether gene order (collinearity) and gene proximity have been maintained or not.

Language:PythonGPL-3.07 1 1

PanSyn

Language:Perl6 10

N50.sh

bash script to quickly produce some assembly stats

Language:ShellMIT4 20

QDiffusion.jl

Leveraging the full dimensionality of single-cell transcriptomics (among other things!)

Language:JuliaApache-2.04 40

mitoPolishCLR

The Mitogenome Assembly Pipeline for CLR + Illumina Ag100Pest

Language:ShellNOASSERTION3 1 4

3Dviewer_TrackVisualization

Language:Java2 20

cilia_HCI

CellProfiler scripts for analysis of cilia and other cellular components from high throughput confocal imaging

GPL-3.01 10

SpCLUST

Spectral Clustering for biological sequences

Language:PythonGPL-3.0101

proch-n50

Perl Module and Utility to calculate N50

Language:PerlGPL-3.01 10