GuideScan specifications

Unique identifier:
OMICS_16793
Restrictions to use:
None
Input format:
BED, GFF/GTF, TXT
Programming languages:
Python
Version:
1.0
Maintained:
Yes
Interface:
Web user interface
Input data:
The genomic coordinates, the user’s parameters.
Output data:
A pre-defined number of gRNAs or gRNA pairs for each genomic coordinate.
Computer skills:
Basic
Stability:
Stable

GuideScan distribution

download

GuideScan specifications

Unique identifier:
OMICS_16793
Interface:
Command line interface
Input data:
The genomic coordinates, the user’s parameters.
Output data:
A pre-defined number of gRNAs or gRNA pairs for each genomic coordinate.
Programming languages:
Python
Stability:
Stable
Maintained:
Yes
Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
BED, GFF/GTF, TXT
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Requirements:
SAMtools, coreutils: specifically shuf, rename, easy_install, biopython, pysam, pyfaidx, bx-python

versioning

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GuideScan distribution

download

GuideScan support

Documentation

Maintainer

  • Andrea Ventura <>
  • Andrea Ventura <>

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Credits

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Publications

Institution(s)

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, NY, USA

Funding source(s)

This work was supported in part by NIH: grants P30-CA008748 (MSK Core), U01-HG007033, U01-HG007893, and by grants from the Geoffrey Beene Cancer Research Foundation, the Uniting Against Lung Cancer Foundation, the Cycle for Survival Foundation, the Pershing Square Sohn Cancer Research Alliance, and the Lung Cancer Research Foundation.

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