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Saket Choudhary

Login: saketkc

Company: University of Southern California

Location: Los Angeles, CA

Bio: /dev/null

Blog: http://saket-choudhary.me/pertinent-blog

Member of

Repositories

afb-image-processor: A GUI based too to analyse TB Smear Samples
altair: Declarative statistical visualization library for Python
bcbio-nextgen: Validated, scalable, community developed variant calling and RNA-seq analysis
bioconda-recipes: Conda recipes for the bioconda channel.
biojs: A library of JavaScript components to represent biological data
biojs-demos: Handpicked components for cool hacks
biojs-genetic-variation-viewer: :recycle: BioJS1.0 Component for visualising human gentic variations, GSoC2014
biojs-vis-hgv: :recycle: BioJS2.0 Human Genetic Variation Viewer
biopython: Official git repository for Biopython (converted from CVS)
biopython-2: null
biopython.github.io: Source of biopython.org website, migrated from MediaWiki
biopython-old: Old screwed up version of my biopython clone
biosql: null
bio-tricks: :syringe: Custom bio* stuff
blather-bot: Source code for aardvark@jabber.org. IIT Bombay Jabber Bot
brewer: Homebrew Personal recipes
bsub_jupyter: Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.
ChIP-seq-analysis: null
clipper: A tool to identify CLIP-seq peaks
comp-bio: null
conda-recipes: Custom recipes
coursera: Couresra codes
dcpp.js: :wrench: DC++ straight from your Browser! No Sharing Required!
deep_learning_papers: A place to collect papers that are related to deep learning and computational biology
dnaplotlib: DNA plotting library for Python
dotfiles: Collection of dotfiles
dropbox_on_sms: Access DropBox files using SMS
dynamic-time-warping: DTW in Python
ECBLASTRestful: null
errata: Errata from Books
extract-transcript-regions: For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and CDS).
fake-coder: Fakes your Code
fos-proposals: :gift_heart: :penguin: Expressing love for Open Source | Archive of GSoC proposals
galaxy-hub: Galaxy Community Hub
galaxy_tools: My Galaxy Wrappers
gencode_regions: Extract 3'UTR, 5'UTR, CDS, Promoter, Genes from Gencode files
ggd: null
ggd-cli: The command-line interface to GGD
ggd-recipes: Recipes for GGD
ggd-recipes-1: conda recipes for genomic data
Google-AppEngine-Projects: All Google-AppEngine Projects that I did. Try out the links at foldername.appspot.com
harmonica-notes: :musical_keyboard: Mostly Hindi Songs
haskell99: Haskell 99 Problems' Solutions
hatex: :school_satchel: => :books: => :floppy_disk: => :mortar_board: 'h'omeworks, 'a'ssignments 'tex'
homebrew: The missing package manager for OS X.
homebrew-dupes: :two_women_holding_hands: System duplicate formulae for the Homebrew package manager
homebrew-linuxbrew-versions: Linux supported homebrew versions
homebrew-science: Scientific formulae for the Homebrew package manager
htseq: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
iclip-seq-snakemake: Snakemake based pipeline for analysing iCLIP-Seq data
ideone-chrome-extension: A chrome extension that allows running code on ideone simply by selecting the text in a browser window
iitb-library-sms-interface: Sends automated SMSes reminiding you of the Due Dates !
impress.js: It's a presentation framework based on the power of CSS3 transforms and transitions in modern browsers and inspired by the idea behind prezi.com.
kicad-ngspice: :electric_plug: Some tweaks integrated in a python script to make kiCAD and ngspice compatible to each other
launchpad: Repo for MLCASS Kaggle Project
limix: null
linuxbrew: A fork of Homebrew for Linux
machine_learning: My experiments with ML
math-501-project: :notebook: Optimal Control Design of a Reparable Multistate system
math578b: course material for Computational Molecular Biology
math-screening-solutions: :green_book: :mortar_board: Solutions for MATH Screening Exams
matplotlib: matplotlib: plotting with Python
MethBase: MethBase maintenance scripts and docs
MG-RAST-Tools: Repository of script tools, examples, and contributed code for using the MG-RAST API
mne-python: MNE : Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
moca: :m: Tool for motif conservation analysis
moca-scripts: Scripts for moca
moca_web: :m: Code for MOtif Conservation Analysis
moodi-hack: Post for Hp !
moodle-stack: Allows you to download moodle files for all your courses. This will grow into a website later
moralistic-motifs: Review of motif finders with a focus on phylogenetic footprinting
motif-logos-matplotlib: Motif logos in matplotlib (POC)
msCentipede: A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
multiZ-scripts: Snakefiles/Python scripts to create conservation tracks
NGS-Stuff: My Experiments with python[BioPython] for NGS Analysis
notebooks: :green_book: Jupyter notebooks for demo/projects, now that github supports them
notes: Coursera Notes
oerpub.remix: null
oerpub.rhaptoslabs.swordpushweb: SWORD upload client with a web interface
oerpub.rhaptoslabs.swordpushweb-buildout: Buildout for development of oerpub.rhaptoslabs.swordpushweb
open-ehr-django: An Electronic Health Records System in *pure* Django.
openmusictheory.github.io: A growing, online "textbook" for music theory and aural skills
overheard-at-hospital: Overheard conversations at a cancer centre
overleaf-cloner: Clone your Overleaf.com projects at once!
pbs-torque: null
perlserial: Automatically exported from code.google.com/p/perlserial
pertinent-blog: :floppy_disk: => :satellite: My answers and others picked up from stackexchange: http://stats.stackexchange.com/users/11668/rightskewed ||
pertinentR: trivial R utils
piddling-pertinent: Those little proofs
piranha: Piranha is a peak-caller for CLIP- and RIP-seq data
pivotal_email_tracker_bot: Send Stories to pivotal through emails !
pivotal-tracker-email-wrapper: :mailbox_closed: Ruby Wrapper to assign tasks on pivotal through an email
plastid: Position-wise analysis of sequencing and genomics data
points-of-significance: Python notebooks for Nature's Point of Significance collection: http://www.nature.com/collections/qghhqm/pointsofsignificance
pomegranate: Graphical models for Python, implemented in Cython for speed.
practice: null
primers: Collection of 'primer/review' articles
protein_loop_closure: Protein Loop Closure Algorithm
pybedtools: Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
pyjoyplot: POC for a 'joyplot' using matplotlib
pyseqlogo: Python package to plot sequence logos
pywt: PyWavelets - Wavelet Transforms in Python
qstat-hpc-cmb-usc: Track running jobs on USC's hpc
Rdatasets: An archive of datasets distributed with R
resume: :hourglass_flowing_sand: Bragging maximus
review: Review of Scientific Papers
riboHMM: A mixture of hidden Markov models to infer translated sequences using ribosome footprint profiling
ribopod: Visualziation interface for riboraptor
riboraptor: Tool for ribo-seq analysis
riborex: Riborex: Fast and flexible identification of differential translation from Ribo-seq data
ribo-seq-snakemake: Snakemake pipeline for Ribo-Seq analysis
riddler: 538 -- We all need stimulants.
rmap: Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)
rna-seq-snakemake: Snakemake based pipeline for RNA-Seq analysis
rnn-cds-prediction: Prediction of CDS regions using RNNs
rss-graduate-diploma-solutions: Solutions to Royal Statistical Society's Graduate Diploma in Statistics Examination
saketkc.github.io: Soure code for http://saket-choudhary.me
scikit-learn: scikit-learn: machine learning in Python
scilab_cloud: :cloud: Scilab on Cloud
scilab_cloud_interface: null
scilab_on_aakash: Scilab on AAKASH
scilab-on-cloud: null
scilab-on-cloud-chrome-extension: A chrome extension that allows running scilab code on cloud simply by selecting the text in a browser window
scipy-presentation: null
scrape_ebi: Automate Submissions To EBI portals
seQer: -Seq Profiler
serialperl: Automatically exported from code.google.com/p/serialperl
SlideShare-Instant: Instant Search for SlideShare Documents
SlideShare-Instants: Instant Search for SlideShare Documents
SPOJ: Spoj/CdeChef ruby solutions
SPOJ_haskell: HAskel Solutions for SPOJ
sra_downloader: A pure python way of downloading those reads
staged-recipes: A place to submit conda recipes before they become fully fledged conda-forge feedstocks
statsmodels: Statsmodels: statistical modeling and econometrics in Python
talks: Monologues. mostly.
tcga-python: Python Wrapper for TCGA API
TF_chipseq_pipeline: AQUAS TF ChIP-seq pipeline
ug_acads: UG Acads IIT B Open Sourced !
ugc-predatory-journal-analysis: UGC's preferred list is predatory
UMI-tools_pipelines: Pipelines for re-analysis of iCLIP and scRNA-Seq data for UMI-tools publication
usc-course-search: Commandl ine course search
usc-math-505A-screening-solutions: Solutions to USC's MATH-505A Screening Exams
usc-math-541A-screening-solutions: Solutions to USC's MATH-541A Screening Exams
usc-math-541B-screening-solutions: Solutions to USC's MATH-541b Screening Exams
usc-vpn-linux-setup: Instructions for accessing USC's VPN on linux
variational-autoencoders-tf-eager: Variational autoencoders using Tensorflow's eager API
wavelets-mixed-models: null
zinba: Unofficial clone of ZINBA from https://code.google.com/p/zinba/

Commits To

Repository	Most Recent Commit	# Commits
saketkc/tcga-python	2014-04-29 01:48:25.0	7
saketkc/galaxy_tools	2014-12-18 11:16:57.0	254
gogetdata/ggd-recipes	2016-05-26 01:44:09.0	1
ISA-tools/bioconda-recipes	2017-12-07 09:34:53.0	3

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.