List of software/websites/databases/other stuff for genome engineering
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Jun 20, 2024
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crispr-cas9
Here are 75 public repositories matching this topic...
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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May 17, 2019 - Python
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
sequencing alignment crispr-analysis variant-calling pcr tracy crispr-cas9 sanger-chromatograms indel-discovery chromatogram sanger-trace-alignment sanger-sequencing pcr-products genetic-engineering indel
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Oct 31, 2024 - C++
CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
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Feb 15, 2024 - Python
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
computational-biology crispr-cas9 single-cell-rna-seq lineage-tracing single-cell-lineage-tracing computational-phylogenetics
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Nov 2, 2024 - Python
FlashFry: The rapid CRISPR target site characterization tool
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Jun 12, 2024 - Scala
Core code for the DeepHF prediction tool
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Jul 23, 2019 - Jupyter Notebook
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
sequencing variants alignment crispr-analysis indigo variant-calling pcr indels crispr-cas9 sanger-chromatograms indel-discovery alleles gear-genomics sanger-sequencing pcr-products chromatogram-traces
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Oct 31, 2024 - JavaScript
Flexible analysis of high-content CRISPR screening
crispr-analysis crispr phenotypes crispr-cas9 functional-genomics ngs-analysis perturbation-screen sequencing-data crispr-cas12
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Dec 19, 2024 - Python
Comprehensive design of CRISPR gRNAs for nucleases and base editors
bioconductor crispr crispr-target crispr-cas9 grna grna-sequence bioconductor-package sgrna crispr-design sgrna-design grna-sequences genomics-analysis
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Jul 18, 2024 - R
A software tool for personalized and allele-specific CRISPR editing.
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Feb 1, 2022 - Jupyter Notebook
SPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.
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Jul 17, 2021 - Python
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
genomics bioconductor crispr crispr-target crispr-cas9 grna grna-sequence bioconductor-package scoring-algorithm sgrna crispr-design sgrna-design grna-sequences
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Oct 4, 2024 - Python
Analysis package for processing counts from genome-wide CRISPR/Cas9 screens
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Feb 19, 2021 - Python
Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing
enzyme mutation protein fitness-landscape crispr-cas9 protein-engineering base-editing llm large-language direct-evoluation direct-evolution large-langage-models
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Jun 6, 2024 - Jupyter Notebook
Modelling insertion efficiency for Prime Insertion Experiments
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Apr 1, 2024 - Python
a guideRNA database generation tool
bioinformatics cpp biology computational-biology bioinformatics-pipeline crispr crispr-cas9 grna bioinformatics-tool crispr-design
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Sep 16, 2024 - C++
A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data
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Feb 1, 2024 - R
CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.
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Oct 18, 2021 - Python
Analyze CRISPR and shRNA functional genetic screening data
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Nov 15, 2024 - Nextflow
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