Search Results for "crispr/cas9"
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Showing 23 open source projects for "crispr/cas9"
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CrisprVi
A Python package for visualizing and analyzing CRISPR sequences
CrisprVi is a Python package for visualizing and analyzing CRISPR sequences. -
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MaChIAto Example Files
The example files of MaChIAto
MaChIAto (Microhomology-associated Chromosomal Integration/editing Analysis tools); a comprehensive analysis software that can precisely classify, deeply analyze, correctly align, and thoroughly review the targeted amplicon sequencing analysis data obtained by various CRISPR experiments, including template-free gene knock-out, short homology-based gene knock-in, and even a new-class CRISPR methodology, Prime Editing. In this repository, we provide the example files of MaChIAto. You can use them as input of the MaChIAto and refer to the output data of MaChIAto. -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. ... -
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RAVI-CRISPR
A bioinformactic tool for CRISPR-based nucleic acid detection.
Rapid detection of nucleic acids is integral to applications in clinical diagnostics and biotechnology. We have developed a bioinformatics tool, named MagicEye, which is an android application to analysis RAVI-CRISPR result. -
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MoPAC
The Modular Pipeline for the Analysis of CRISPR screens
To facilitate the comparison of gene essentialities in two or more cell samples, we propose MoPAC (Modular Pipeline for Analysis of CRISPR screens), a Shiny-driven interactive tool for differential essentiality analysis in CRISPR/Cas9 screens. For installation and usage instructions please refer to the wiki page. -
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CRISPRtrack
Using CRISPR spacer content for bacterial species tracking
CRISPRtrack uses CRISPR spacers as molecular markers to track bacterial strains. It can be used to estimate the microbiome similarity based on the sharing of CRISPR spacer contents between the microbiomes. It can also be used to quantify the retention of donor strains in recipients that receive microbiota transfer treatment (such as fecal microbiota transfer, FMT) using microbiome data. -
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CRISPRamplicon
A tool for analysis of Genome editing outcomes from sequencing data
...In particular, we have developed a new bioinformatics tool named CRISPRamplicon, which can be used for analysis of CRISPR/Cas9 genome editing outcomes for high-throughput sequencing data with fast speed. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. -
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sgRNAcas9
a software for designing CRISPR sgRNA and evaluating Off-Target Sites
This package consists of programs to perform a search for CRISPR target sites (protospacers) with user-defined parameters, predict genome-wide Cas9 potential off-target cleavage sites (POT), classify the POT into three categories, batch design oligonucleotides for constructing 20-nt (nucleotides) or truncated sgRNA expression vectors, extract desired length nucleotide sequences flanking the on- or off-target cleavage sites for designing PCR primer pairs to validate the mutations by T7E1 cleavage assay. ... -
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Protospacer Workbench
CRISPR/Cas9 guide-RNA design
Protospacer Workbench helps to design, analyze, and share CRISPR target-sites for any organism or set of FASTA formatted sequences. Design of guide-RNAs for the CRISPR/Cas genome editing system is intuitively easy, but computationally difficult. The main difficulty arises from the need to identify potential off-targets that may be quite different from the intended target. Current online tools for guide-RNA design provide a user friendly interface to sequence mapping software such as Bowtie or BLAST. ... -
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An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases. Cas-OFFinder is an ultrafast and highly versatile off-target searching tool. Importantly, Cas-OFFinder is written in OpenCL, enabling operation in diverse platforms such as central processing units (CPUs), graphics pro-cessing units (GPUs), digital signal processors (DSPs), and other processors.
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CRISPR-Offinder
a CRISPR guide RNA design and off-target searching to
...Availability: CRISPR-offinder is freely available at http://crispr-offinder.com/ or http://crispr.igenetech.com/. -
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NgAgo-gDNA
A tool for designing NgAgo gDNA for genome editing
...NgAgo binds 5' phosphorylated single-stranded guide DNA (gDNA) of ∼24 nucleotides, efficiently creates site-specific DNA double-strand breaks when loaded with the gDNA. The NgAgo-gDNA system does not require a protospacer-adjacent motif (PAM), as does Cas9(Gao et al., 2016 Nat Biotechnol). Based on these features, NgAgo-gDNA was developed, which is a bioinformatic tool for fast designing gDNA and evaluating potential off-target cleavage sites. 2. Where is the homepage of NgAgo-gDNA? www.ngago-gdna.org (in prepare) or http://www.biootools.com/col.jsp?id=178 NgAgo-gDNA design source code free for academic, nonprofit, and personal use. ... -
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BAGEL: analysis of gene knockout screens
BAGEL: Bayesian Analysis of Gene EssentiaLity
BAGEL: software for Bayesian analysis of gene knockout screens using pooled library CRISPR or RNAi. BAGEL is a Bayesian classifier for pooled library genetic perturbation screens, using either CRISPR-Cas9 or shRNA libraries. It uses training sets of known essential and nonessential genes to estimate what the fold change distribution of an essential or nonessential gene should look like. Then, for each uncharacterized gene, it takes all observations of reagents targeting that gene (guide RNA, for CRISPR-Cas9 screens, or short hairpin RNA) and makes a probabilistic statement about whether those observations were more likely drawn from the essential or nonessential training set. ... -
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CT-Finder
A Web Service for CRISPR Optimal Target Prediction and Visualization
...A visualization of on-target and off-target matches against the chosen reference genome is provided in JBrowse. [1] Who are we? Please visit our website http://bioinfolab.miamioh.edu [2] How to cite CT-Finder? Zhu, H. et al. CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization. Sci. Rep. 6, 25516; doi: 10.1038/srep25516 (2016). http://www.nature.com/articles/srep25516 [3] CT-Finder Installation manual For user manual, please visit the Wiki page of this website. [4] CT-Finder Q&A For Q&A, please visit the Blog page of this website. [5] CT-Finder bug report You can report a bug as a Ticket request. -
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SSC
Spacer Scoring for CRISPR
SSC is a tool for predicting sgRNA efficiency from spacer sequences. It supports the applications of optimizing sgRNA libraries in CRISPR/Cas9 knockout or CRISPR/dCas9 inhibition/activation screens. -
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Mining CRISPRs in Environmental Datasets MinCED is a bioinformatic program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the command-line and was derived from CRT (CRISPR Recognition Tool). The development of MinCED takes place at https://github.com/ctSkennerton/minced
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Protospacer
Rapid gRNA design and validation for CRISPR
Sign up to our mailing list at http://www.protospacer.com/contact.html. Protospacer allows researchers to build, analyze, and share their own database of CRISPR target-sites. This enables the development of custom libraries and helps to transfer the CRISPR technology to new organisms. Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. ... -
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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