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3ca

Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".

awesome-deep-learning-single-cell-papers

ceres-solver

A large scale non-linear optimization library

deeplm

DeepLM: Large-scale Nonlinear Least Squares on Deep Learning Frameworks using Stochastic Domain Decomposition (CVPR 2021)

deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

dpa-analysis

Nextflow Pipeline for the analysis of Double Progressive Alignment (DPA)

edward

A library for probabilistic modeling, inference, and criticism. Deep generative models, variational inference. Runs on TensorFlow.

fdrnet

A method for identifying significantly mutated subnetworks in human diseases

fnc-extras

Extra materials for *Fundamentals of Numerical Computation* by Driscoll and Braun.

generative-ai-for-beginners

12 Lessons, Get Started Building with Generative AI 🔗 https://microsoft.github.io/generative-ai-for-beginners/

goatools

Python scripts to find enrichment of GO terms

hope

SIGMOD 2024 paper titled "Efficient High-Quality Clustering for Large Bipartite Graphs"

ir-query-clustering

local-densely-connected-clusters

Code to accompany the paper "Local Algorithms for Finding Densely Connected Clusters", published at ICML 2021.

localgraphclustering

locfdr-python

Python implementation of Efron, Turnbull, and Narasimhan's R function locfdr v1.1-7, which computes local false discovery rates. See http://cran.r-project.org/web/packages/locfdr/ for more information.

multifdrnet

An algorithm to detect significantly disrupted subnetwork using multiplex networks.

multilayer-networks-library

personalized_pca

An implementation for personalized PCA

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

pytorch-minimize

Newton and Quasi-Newton optimization with PyTorch

qpsolvers

Quadratic Programming solvers in Python with a unified API

rbm-dp-experiment

Simplistic RBM and DP

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

sharepathway

a python package for KEGG pathway enrichment analysis with multiple gene lists.

snlls

Stochastic Nonlinear Least-Squares for Large-Scale Machine Learning

specgreedy

Unified Dense Subgraph Detection Algorithms: **Best student DM paper award in ECML-PKDD'20**

tsgraph

xylearn

A simplified version of pylearn2