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actionet

ACTIONet single-cell analysis framework

adaptive-lif-population-model

The Delphi model of adaptive population of leaky integrate-and-fire neurons

ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

ads1-slides

Slides for Algorithms for DNA Sequencing Coursera class

all-active-manuscript

Code for reproducing the figures presented in: Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types

allensdk

amnon-tracking

Comparision between Amnon and Chris data

anndata2ri

Convert between AnnData and SingleCellExperiment

atlasplot

Reproducible Plots for the Allen Institutes Brain Atlases

awesome-single-cell

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

bbknn

Batch balanced KNN

benchmark

Comparison of single-cell normalization methods using multiple datasets with ground-truth labels

biogpt

biovis

biovis simulator visualization toolbox

bluepyopt

Blue Brain Python Optimisation Library

bmtk

Brain Modeling Toolkit

btmorph_v2

btmorph v2. Object-oriented library to analyze neuronal structure

ca-imaging-extraction

This page collect all the links to the code that might be reused in the future studies. You are welcome to contribute your own section that might be useful for anyone else in their research.

ca-spike-extraction-and-svm-decoder

ML spike algorithm and SVM decoder predicting the drifting gratings direction based on optical recordings in V1 visual cortex.

cell-types

celloracle

This is the alpha version of the CellOracle package

cellphonedb

cellphonedb-1

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

cellxgene

An interactive explorer for single-cell transcriptomics data

cellxgene_vip

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

clei2block

Deep-neural protein translation

code_snippets

A repo with random short code snippets

compass

Vector representations of gene co-expression in single cell RNAseq.

course-content

Summer course content for Neuromatch Academy