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atg_crispr_score_calculator

This program takes three commandline arguments: (1) CFD scores for mismatches/bulges/PAMs (in a tab-delimted text file), (2) a crRNA sequence, and (3) a DNA sequence as input, processes and compares them, and outputs a calculated CFD score.

atg_fastq_demultiplexer

A python script that splits fastq files according to a provided tsv file containing the name of fastq samples, their barcode sequences (begining and end of lines), and their demuxed name.

atg_fastq_merger

A python script that merges illumina NGS paired-end reads using FLASH, collects and save the combination stats in a table.

atg_htmltools-csv-to-datatable

Render any csv/tsv file into a responsive, sortable, and searchable HTML datatable without any server-side scripting. A url parameter will be used to point to the CSV file. It can be used as general purpose tool.

atg_molbio_excel

An Excel file for Molecular Biologists' day-to-day use. Conveniently provides useful functions from basic ReverseComplement, and Translate functions to sophisticated Needleman alignment and Motif Searches.

atg_sgrna_annotator

An Excel-based tool to annotate CRISPR sgRNAs from literature on a RefSeq genbank file for a given Human or Mouse gene. It can be used for general annotation purposes, too! Both Mac and Windows are supported.

behboxrokh.github.io

cas-offinder

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

ghahfarokhi

ghahfarokhi.github.io

Personal portfolio/resume webpage

ncbi_batch_download

Download and annotate the RefSeq for a large set of genomic coordinates using an Excel workbook.

rima

Rational Indel Meta-Analysis (RIMA); An Excel-based tool for mutational pattern analysis.