Pinned Repositories
229-E-Corona-Genome-Analysis
Genome Analysis of 229-E COVID-19 strain
ACAM
This is the R package ACAM for cell annotation.
ACAMdata
alexa-seq
ALEXA-seq - alternative expression analysis by RNA-seq
content
Official content for Harvard CS109
nbahti's Repositories
nbahti/APEC
Single cell epigenomic clustering based on accessibility pattern
nbahti/ascend
Analysis of Single Cell Expression, Normalization and Differential expression
nbahti/biopython-coronavirus
Biopython Jupyter Notebook tutorial to characterize a small genome
nbahti/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
nbahti/cisTopic
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
nbahti/cobaya
Code for Bayesian Analysis in Cosmology
nbahti/Comparison_batch_remove_softwares
code used for article - Comparison of Scanpy-based algorithms to remove the batch effect of single-cell RNA-seq data
nbahti/DCC
This repository contains the source code and data for reproducing results of Deep Continuous Clustering paper
nbahti/fly-atac
Code relevant to sci-ATAC-seq of Drosophila embryogenesis.
nbahti/GEMSEC
The TensorFlow reference implementation of 'GEMSEC: Graph Embedding with Self Clustering' (ASONAM 2019).
nbahti/kallisto
Near-optimal RNA-Seq quantification
nbahti/keras
Deep Learning for humans
nbahti/libsvm
nbahti/pagoda2
R package for analyzing and interactively exploring large single-cell RNA-seq datasets
nbahti/pCreode
An algorithm for mapping cell state transitions.
nbahti/perl-rna-seq-star
STAR + HTSeq + featureCounts RNA-seq processing pipeline environment and wrapper script, including SRA query, download, and caching functionality and useful reuse/restart features
nbahti/pyrcc
Python implementation of Robust Continuous Clustering
nbahti/rnaseqGene
RNA-seq workflow: gene-level exploratory analysis and differential expression
nbahti/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
nbahti/scHCL
nbahti/scikit-learn
scikit-learn: machine learning in Python
nbahti/scRNAseqWorkflow
Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz
nbahti/scVI
Deep generative modeling for single-cell transcriptomics
nbahti/SIMLR
Implementations in both Matlab and R of the SIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/nmeth.4207
nbahti/single-cell-rnaseq-analysis
A guide for analyzing single-cell RNA-seq data using the R package Seurat. Go from raw data to cell clustering, identifying cell types, custom visualizations, and group-wise analysis of tumor infiltrating immune cells using data from Ishizuka et al. Nature 2019.
nbahti/sleuth
Differential analysis of RNA-Seq
nbahti/SnapATAC
Single Nucleus Analysis Pipeline for ATAC-seq
nbahti/SnapTools
A module for working with snap files in Python
nbahti/SUPPA
SUPPA2: Fast quantification of differential splicing
nbahti/VAE-GMVAE
This repository contains the implementation of the VAE and Gaussian Mixture VAE using TensorFlow and several network architectures