shansabri Goto Github PK

academic-kickstart

Academic template adapted for Hugo static site generator.

binhouse

A collection of useful little tools & code snippets without a home

bioperl

Perl/BioPerl Scripts from JHU AS.410.698.81.SP13

cayman-theme

A responsive theme for GitHub Pages

clipper

A tool to identify CLIP-seq peaks

cronjob

⌛ A workaround to permanently store file under the global scratch file system mounted on the Hoffman2 Cluster

deconr

A computational method for inferring individual cell type ChIP-seq profiles from population ChIP-seq and single cell RNA-seq data

drlib

Personal R package

dropseq_runner

A collection of scripts to processing single cell sequencing reads to DGE

fmm

〰️ My attempt at fitting Finite Mixture Models from scratch

iclip

✂ A few scripts used to demultiplex and process iCLIP data

iguide

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

jubri

🧩 A method for literature-based keyword ontology

microarray-analysis

R scripts

modified-levenshtein

🔤 A direct and efficient translation of the dynamic programming algorithm of the Sequence-Levenshtein distance into Cython

orifinder

🎯 Pinpoint the origin of replication (oriC) for bacterial genomes

practical-concepts-bfx

Basic Perl/BioPerl Scripts

pubmedscraper

📚 R Package for scraping PubMed abstracts for most frequently occurring words associated with a keyword

pyspark-clustering

K-means clustering algorithm in MLlib via PySpark

pyspark-movie-recommender

🎬 Utilizing PySpark's Alternating Least Squares (ALS) algorithm for model-based movie recommendations.

rainbow-analysis

Reproducible analysis of our Rainbow manuscript

rismed

RISmed is an R package for downloading and analyzing data from the NCBI databases

rpkg-skeleton

baseline skeleton framework for a R pkg

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

shansabri

shansabri.github.io

My online treefort

slncky

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

SRA Tools

ssfold

🧬 A Dynamic Programming Algorithm for Predicting Optimal RNA Secondary Structure

svm-rfe

An R implementation of the (multiple) Support Vector Machine Recursive Feature Elimination (mSVM-RFE) feature ranking algorithm