Shan Sabri's Projects
Academic template adapted for Hugo static site generator.
A collection of useful little tools & code snippets without a home
Perl/BioPerl Scripts from JHU AS.410.698.81.SP13
A responsive theme for GitHub Pages
A tool to identify CLIP-seq peaks
⌛ A workaround to permanently store file under the global scratch file system mounted on the Hoffman2 Cluster
A computational method for inferring individual cell type ChIP-seq profiles from population ChIP-seq and single cell RNA-seq data
Personal R package
A collection of scripts to processing single cell sequencing reads to DGE
〰️ My attempt at fitting Finite Mixture Models from scratch
✂ A few scripts used to demultiplex and process iCLIP data
Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
🧩 A method for literature-based keyword ontology
R scripts
🔤 A direct and efficient translation of the dynamic programming algorithm of the Sequence-Levenshtein distance into Cython
🎯 Pinpoint the origin of replication (oriC) for bacterial genomes
Basic Perl/BioPerl Scripts
📚 R Package for scraping PubMed abstracts for most frequently occurring words associated with a keyword
K-means clustering algorithm in MLlib via PySpark
🎬 Utilizing PySpark's Alternating Least Squares (ALS) algorithm for model-based movie recommendations.
Reproducible analysis of our Rainbow manuscript
RISmed is an R package for downloading and analyzing data from the NCBI databases
baseline skeleton framework for a R pkg
Single-Cell Analysis in Python. Scales to >1M cells.
My online treefort
slncky is a tool that filters a set of transcripts for bona-fide long non-coding RNAs and discovers long non-coding RNA orthologs.
SRA Tools
🧬 A Dynamic Programming Algorithm for Predicting Optimal RNA Secondary Structure
An R implementation of the (multiple) Support Vector Machine Recursive Feature Elimination (mSVM-RFE) feature ranking algorithm