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single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

single_cell_analysis

Introduction to single-cell RNA-Seq analysis workshop

single_cell_analysis-1

Documents used for workshops on single cell analysis

single_cell_deg

single_site_cavity_model

3D CNN predicting protein residues' identity and change-of-stability of single-site mutants.

singlecelltk

sire

Sire Molecular Simulations Framework

sire_edecomp

Sire scripts to post-process a trajectory and perform per-residue interaction energy decomposition analysis

sirms

Simplex representation of molecular structure - a chemoinformatic tool for calculation of simplex descriptors

siteinterlock

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

sivs

An iterative feature selection method that internally utilizes varius Machine Learning methods that have embeded feature reduction in order to shrink down the feature space into a small and yet robust set.

skin-data-augmentation

Source code for the paper 'Data Augmentation for Skin Lesion Analysis' - Best Paper Award at the ISIC Skin Image Analysis Workshop @ MICCAI 2018

skl_kta

Parameter-Free Spectral Kernel Learning

sknifedatar

sknifedatar is a package that serves primarily as an extension to the modeltime 📦 ecosystem. In addition to some functionalities of spatial data and visualization.

slemi

Statistical Learning based Estimation of Mutual Information. R CRAN package.

slider

Sliding Window Functions

slimrec

Sparse Linear Method to Predict Ratings and Top-N Reccomendations

slope

Sorted L1 Penalized Estimation

slpmf

Fast Non-negative Matrix Factorization under KL-Divergence: A Case for Link Prediction

smallk

High-performance Non-negative Matrix Factorizations (NMF) - Python/C++

smi2sdf3d

3D diverse conformers generation using rdkit

smiles-enumeration

SMILES enumeration for QSAR modelling using LSTM recurrent neural networks

smilesbasedsimilaritykernels

smilesdrawer

A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license.

smina

smina-docking-benchmark

smmr-machine-learning-data-generating-processes

R code for simulating data under different machine learning methods based on SMMR paper (2021)

snakemake_dna-seq_tutorial

Use snakemake via Binder

snap

Stanford Network Analysis Platform (SNAP) is a general purpose network analysis and graph mining library.