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py-motmetrics

:bar_chart: Benchmark multiple object trackers (MOT) in Python

kraken2

The second version of the Kraken taxonomic sequence classification system

OpenBioMed

infercnv

Inferring CNV from Single-Cell RNA-Seq

maxvit

[ECCV 2022] Official repository for "MaxViT: Multi-Axis Vision Transformer". SOTA foundation models for classification, detection, segmentation, image quality, and generative modeling...

SpliceAI

A deep learning-based tool to identify splice variants

omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

scFoundation

ShinyCell

Shiny Interactive Web Apps for Single-Cell Data

GPTCelltype

TOSICA

Transformer for One-Stop Interpretable Cell-type Annotation

indrops

Pipeline for processing inDrops sequencing data

DeepLoc

This repository contains the code, and access to the pretrained models and datasets for the paper: "Automated analysis of high-content microscopy data with deep learning"

scRNAseq_cell_cluster_labeling

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

long-read-rna-pipeline

ENCODE long read RNA-seq pipeline

SingCellaR

an integrative analysis tool for analysing large-scale single cell RNA-sequencing data

devCellPy

devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.

OrganoID

MarcoPolo

MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-seq data

HUBDesign

Hierarchical Unique Bait Design for simultaneous and specific capture of known and novel targets

FCA_bone_marrow

This repository contains all analysis scripts used to explore single cell datasets for: Jardine and Webb et al., 2021, "Blood and immune development in human fetal bone marrow and in Down syndrome" (Nature, 2021).

SPiP

Splicing Prediction Pipeline

pyMN

Python Implementation of MetaNeighbor scRNAseq Analysis Method

neuronal-cell-type-classification

2021-edition-available-colabs

Colab Notebooks implementing training and inference for the methods of several contestants participating in the 2021 CTC edition, in order to fulfill the reusability criteria

QuantificationBioparticle

Facile quantification of nanosized bioparticles in bright-filed micrograph via deep learning

PRS-SIM

Pixel-realignment based self-supervised reconstruction for structured illumination microscopy

MACPnet

Using for the segmentation of organoids

pyrganoid