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Eric Edsinger's starred repositories

whisper

Robust Speech Recognition via Large-Scale Weak Supervision

Language:PythonMIT65025 5420

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

Language:Jupyter NotebookApache-2.045734 303 658

scipy

SciPy library main repository

Language:PythonBSD-3-Clause12757 348 10162

cvat

Annotate better with CVAT, the industry-leading data engine for machine learning. Used and trusted by teams at any scale, for data of any scale.

Language:TypeScriptMIT11920 183 4007

panel

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

Language:PythonBSD-3-Clause4483 57 3481

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Language:PythonMIT3026 65 318

TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Language:PerlGPL-3.0452 22 174

RagTag

Tools for fast and flexible genome assembly scaffolding and improvement

Language:PythonMIT448 8 179

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Language:ShellMIT402 17 309

NextDenovo

Fast and accurate de novo assembler for long reads

Language:CGPL-3.0351 14 203

merqury

k-mer based assembly evaluation

Language:ShellNOASSERTION272 12 127

KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Language:C++GPL-3.0201 23 162

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 61

RNAlysis

Analyze your RNA sequencing data without writing a single line of code

Language:PythonMIT123 4 27

meryl

A genomic k-mer counter (and sequence utility) with nice features.

Language:C111 11 45

mapping_pipeline

Mapping pipeline for data generated using Arima-HiC

Language:PerlMIT67 8 16

ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes

Language:PythonNOASSERTION53 4 52

instaGRAAL

Large genome reassembly based on Hi-C data, continuation of GRAAL

Language:CudaGPL-3.038 8 43

STGRNS

Language:Jupyter Notebook24 20

phyutility

Language:Java21 1 1

pin_hic

A Hi-C scaffolding method

Language:CMIT20 3 14

pbfusion

Language:Python18 50

abSENSE

Code to perform homolog detectability analyses as described in Weisman et al. 2020 (https://www.biorxiv.org/content/10.1101/2020.02.27.968420v1)

Language:Python17 1 1

polishCLR

A nextflow pipeline for polishing CLR assemblies

Language:Nextflow16 4 30

HapPy

Haploidy and Size Completeness Estimation

Language:PythonMIT13 2 2

DeepBIO

Language:Python800

DeepBIO

Language:Python401

mitoPolishCLR

The Mitogenome Assembly Pipeline for CLR + Illumina Ag100Pest

Language:ShellNOASSERTION3 1 4

Cunha_Giribet_2019_ProcRSocB

Code used in Cunha TJ, Giribet G. 2019 A congruent topology for deep gastropod relationships. Proc. R. Soc. B 286: 20182776

Language:HTML300