Pinned Repositories
blog
covmuller
Covmuller is an R-package designed for analysis of SARS-CoV-2 sequencing metadata deposited on GISAID
fos-proposals
:gift_heart: :penguin: Archive of GSoC proposals
gencode_regions
Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files
hatex
'h'omeworks, 'a'ssignments 'tex' for courses at USC
pySCTransform
Python package to perform normalization and variance-stabilization of single-cell data
pyseqlogo
Python package to plot sequence logos
pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
rna-seq-snakemake
Snakemake based pipeline for RNA-Seq analysis
ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
saketkc's Repositories
saketkc/rna-seq-snakemake
Snakemake based pipeline for RNA-Seq analysis
saketkc/hatex
'h'omeworks, 'a'ssignments 'tex' for courses at USC
saketkc/riboraptor
Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)
saketkc/usc-vpn-linux-setup
Instructions for accessing USC's VPN on linux
saketkc/notebooks
:green_book: Jupyter notebooks for demo/projects, now that github supports them
saketkc/scilab_cloud
:cloud: Scilab on Cloud
saketkc/sklearn-hogsvd
Scikit-learn compatible python implementation of HO-GSVD
saketkc/EE-546-project
saketkc/pyFLGLM
saketkc/blog-archive
:floppy_disk: => :satellite:
saketkc/predicting-cds-rnn
saketkc/pyfastnbfit
Fast fitting for counts data using Minka's algorithm
saketkc/re-ribo-smk
Snakemake pipeline for end-to-end Ribo-seq analysis
saketkc/2019_radiation_gbm
saketkc/2020_MCSK
Code for Global Translational Landscape of the Candida albicans Morphological Transition
saketkc/ARMpy
Examples reproduced from ARM from Hill and Gelman
saketkc/azimuth
A Shiny web app for mapping datasets using Seurat v4
saketkc/bioconda-recipes
Conda recipes for the bioconda channel.
saketkc/calculate_mappability
Calculate mappability for hg38/mm10
saketkc/fastpages
An easy to use blogging platform, with enhanced support for Jupyter Notebooks.
saketkc/pca-for-one-and-all
saketkc/pertinentR
trivial R utils
saketkc/probability
Probabilistic reasoning and statistical analysis in TensorFlow
saketkc/pyro-notebooks
saketkc/pyscutils
saketkc/pysradb-manuscript
saketkc/qvalue
Converts p-values in q-values, see (Storey and Tibshirani, 2003)
saketkc/riboHMM
A mixture of hidden Markov models to infer translated sequences using ribosome footprint profiling
saketkc/ribopod
A database of uniformly processed Ribo-seq datasets
saketkc/sra_downloader
A pure python way of downloading those reads