Davide Cittaro's repositories

schist

An interface for Nested Stochastic Block Model for single cell analysis

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scatACC

Things needed for custom scATAC analysis

schist-notebooks

Some example notebooks for scNSBM package

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scTips_Twitter

Some random code about single cell stuff to share with my Tweeps

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anndata

Annotated data matrix.

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awesome-single-cell

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

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bbknn

Batch balanced KNN

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cellrank

CellRank for directed single-cell fate mapping

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dawe.github.io

Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll

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dsptool

A general DSP tool for processing genomic data

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ecosystem-packages

Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

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fit_nbinom

Negative binomial maximum likelihood estimate implementation in Python using L-BFGS-B

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HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

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kallisto

Near-optimal RNA-Seq quantification

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MOFA

Multi-Omics Factor Analysis

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mofapy2

Multi-omics factor analysis v2

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scanpy

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

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schist-feedstock

A conda-smithy repository for schist.

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scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

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scikit-fusion

scikit-fusion: Data fusion via collective latent factor models

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sinto

Tools for single-cell data processing

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staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

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SurpriseMeMore

Module to detect mesoscale structures (community, core-periphery, bipartite) on Graphs and Multigraphs using surprise.

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tensorly

TensorLy: Tensor Learning in Python.

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UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

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