Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: crispr-cas9

Repositories

akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

Language: Perl - Size: 12.5 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 2

westlake-repl/ProteinLM-TDG2-Mutation

Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

Language: Jupyter Notebook - Size: 7.8 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 9 - Forks: 0

davidliwei/awesome-CRISPR

List of software/websites/databases/other stuff for genome engineering

Size: 2.8 MB - Last synced: 4 days ago - Pushed: 3 months ago - Stars: 467 - Forks: 105

ArcInstitute/ScreenPro2

Flexible analysis of high-content CRISPR screening

Language: Python - Size: 3.23 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 7 - Forks: 1

YosefLab/Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

Language: Python - Size: 46.2 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 73 - Forks: 23

LoopGlitch26/CRISPR-consequences

Biotechnology project about possible side effects and consequences of CRISPR

Size: 204 KB - Last synced: 16 days ago - Pushed: about 4 years ago - Stars: 3 - Forks: 0

Russel88/CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

Language: Python - Size: 250 MB - Last synced: 6 days ago - Pushed: 3 months ago - Stars: 86 - Forks: 15

crisprVerse/crisprScore

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Language: Python - Size: 80.7 MB - Last synced: 9 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 2

aaronwtr/interpreting-ml-based-drops

This repository accompanies my research into the interpretability of DNA Damage Repair Outcome Predictors (DROPs). By analyzing these models using interpretability methods, we hope to uncover what features specifically are driving the accuracy of these prediction models.

Language: Python - Size: 2.89 MB - Last synced: 30 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

parthspatel/DeepCas

Deep Learning Cas9 Activity Predictor

Language: Python - Size: 181 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

gear-genomics/tracy

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Language: C++ - Size: 3.17 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 94 - Forks: 19

julianeweller/MinsePIE

Modelling insertion efficiency for Prime Insertion Experiments

Language: Python - Size: 27.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 12 - Forks: 2

lucapinello/CRISPResso 📦

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

Language: Python - Size: 4.93 MB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 129 - Forks: 55

crisprVerse/crisprDesignData

Useful human and mouse data for the crisprVerse ecosystem

Language: R - Size: 213 MB - Last synced: 9 days ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

ZuberLab/crispr-process-nf

Process CRISPR and shRNA functional genetic screening data

Language: Nextflow - Size: 1.57 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 1

clbenoit/CutOneStrand

This tool is designed to scan all positions on a gene than can be used to specifically cut one DNA strand using a given cas9.

Language: Shell - Size: 502 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

crisprVerse/crisprDesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Language: R - Size: 5.84 MB - Last synced: 9 days ago - Pushed: 29 days ago - Stars: 15 - Forks: 4

BIMSBbioinfo/crispr_DART

A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data

Language: R - Size: 26.8 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 10 - Forks: 2

mckennalab/FlashFry

FlashFry: The rapid CRISPR target site characterization tool

Language: Scala - Size: 27.2 MB - Last synced: 3 months ago - Pushed: almost 2 years ago - Stars: 57 - Forks: 10

niekwit/pycrispr

Pip package for CRISPR-Cas9 screen analysis

Language: Python - Size: 1.15 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 2 - Forks: 0

jordiabante/biodive

A reference-free statistical approach to diversity-generating & mobile genetic element discovery

Language: Python - Size: 959 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0

babinyurii/crispr_cas9

NGS data analysis scripts for HBV elimination research group

Language: Python - Size: 5.19 MB - Last synced: 23 days ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 1

lucatorep/sgRNA_design_scripts

Script used to cdesign sgRNA sequences based on desired input parameters comparing different web-based tools

Size: 1.32 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

GilbertLabUCSF/ScreenPro2 📦

[This is an archived repository, see the current version in Arc Institute GitHub]

Language: Python - Size: 125 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1

ZuberLab/crispr-mageck-nf

Analyze CRISPR and shRNA functional genetic screening data

Language: Nextflow - Size: 48.8 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 6 - Forks: 5

SubGlitch1/GuideRNA_Designer

CRISPR Guide RNA Designer

Language: Python - Size: 5.86 KB - Last synced: 5 months ago - Pushed: about 2 years ago - Stars: 6 - Forks: 1

gear-genomics/indigo

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Language: JavaScript - Size: 2.72 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 30 - Forks: 6

pritykinlab/guidescan-cli

A gRNA database generation tool.

Language: C++ - Size: 9.56 MB - Last synced: 24 days ago - Pushed: about 1 month ago - Stars: 12 - Forks: 5

izhangcd/DeepHF

Core code for the DeepHF prediction tool

Language: Jupyter Notebook - Size: 95.3 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 31 - Forks: 13

TuanjieNew/Indel-Finder

A program used to find indels on target gene edited by CRISPR/Cas9

Language: Python - Size: 58.6 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 4 - Forks: 1

tdseher/addtag-project

CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.

Language: Python - Size: 2.67 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 2

schmidt73/guidescan-web

A guideRNA design tool for the modern era.

Language: Clojure - Size: 2 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 7 - Forks: 2

PeterDeWeirdt/gpp-guide-design

CRISPR sgRNA design for the Genetic Perturbation Platform at the Broad Institute

Language: Python - Size: 5.97 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

hyunhwan-jeong/CB2

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.

Language: R - Size: 3.59 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 6 - Forks: 1

naikai/crispr

CRISPR + CCLE heat map

Language: R - Size: 24.4 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

dDipankar/DeepGuide

DeepGuide: a tool to predict CRIPR activity

Language: MATLAB - Size: 26.7 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

sunnyosun/piga-paper-hic-analysis

This repo contains computational analysis performed in Li21.

Language: Jupyter Notebook - Size: 8.79 KB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

casanova-lab/GMUSCLE

Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing

Language: Python - Size: 25.7 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 2 - Forks: 1

jeffmak/crispr-cas9-nanoenv

Accurate prediction of CRISPR-Cas9 off-target activity by learning to utilize internal protein 3D nanoenvironment descriptors

Language: Python - Size: 13.2 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

kuanrongchan/TMEM41B-VMP1-KO

Repository contains information on the mass spectrometry data in TMEM41B and VMP1 KO cells

Language: Jupyter Notebook - Size: 194 KB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 1

crisprVerse/crisprBase

Base functions and classes for CRISPR gRNA design

Language: R - Size: 3.19 MB - Last synced: 9 days ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

nikolapeja6/gi-crispr-cas9

Overview of CRISPR-Cas9 and other gene editing methods - an assignment for the Computational Genomics course at the School of Electrical Engineering, University of Belgrade.

Language: HTML - Size: 113 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

yanwu2014/genotyping-matrices

Assign genotype to cells from scRNA-seq data

Language: Python - Size: 105 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

uzh-dqbm-cmi/PRIDICT

Prime editing guide RNA prediction

Language: Python - Size: 339 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 4

m-jahn/R-notebook-crispri-lib

R markdown notebooks for analysis of CRISPR inhibition library data

Language: Jupyter Notebook - Size: 456 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 3 - Forks: 1

Orpowell/CRISPR-Designer

A tool for designing sgRNAs and repair templates for CRISPR experiments

Language: Python - Size: 1.36 MB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

crisprVerse/crisprBwa

BWA-based alignment of CRISPR gRNA spacer sequences

Language: R - Size: 105 KB - Last synced: 9 days ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

crisprVerse/crisprBowtie

Bowtie-based alignment of CRISPR gRNA spacer sequences

Language: R - Size: 422 KB - Last synced: 9 days ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

snehaiasri/acrcasppi

Prediction of protein-protein interaction between anti-crispr protein (acr) and CRISPR-associated (cas) protein using machine learning algorithm

Size: 9.89 MB - Last synced: 4 days ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

PierreMkt/Dmel-sgRNA-Efficiency-Prediction

Python and R pipeline to predict sgRNA efficiency in D.mel via machine learning algorithms trained and optimized on CRIPSR pooled gene essentiality screens

Language: Python - Size: 30.6 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0