MartinLoza

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Laboratory of Functional Analysis in silico

Tokyo University

https://martinloza.github.io/Canek/

@MartinLozaLopez

Martin Loza's starred repositories

3d-genome-processing-tutorial

A 3D genome data processing tutorial for ISMB/ECCB 2017

Language:Jupyter NotebookMIT4800

hic2cool

Lightweight converter between hic and cool contact matrices.

Language:PythonMIT6100

Canek

Unbiased integration of single cell transcriptomes.

Language:RNOASSERTION500

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

Language:Jupyter NotebookApache-2.01295500

ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

Language:PythonMIT19100

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

MIT300900

singleCellHaystack

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Language:RNOASSERTION7300

seurat

R toolkit for single cell genomics

Language:RNOASSERTION218600

scanorama

Panoramic stitching of single cell data

Language:PythonMIT25400

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

Language:RNOASSERTION50300

mclust

:exclamation: This is a read-only mirror of the CRAN R package repository. mclust — Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation. Homepage: https://mclust-org.github.io/mclust/

Language:R1900

umap

Uniform Manifold Approximation and Projection

Language:PythonBSD-3-Clause721100

scanpy

Single-cell analysis in Python. Scales to >1M cells.

Language:PythonBSD-3-Clause180700

splatter

Simple simulation of single-cell RNA sequencing data

Language:RGPL-3.021000