Project for the Transcriptomic course of "Bioinformatics for Computational Genomics" MSc
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Updated
Sep 3, 2023 - HTML
Project for the Transcriptomic course of "Bioinformatics for Computational Genomics" MSc
This repo contains scripts to analyze Single-Cell RNA-Seq data obtained from human enteriod cell culture.
SimCD: Simultaneous Clustering and condition-specific Differential expression analysis for single-cell transcriptome data
CD24 CART single cell analysis
STREAM: enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
Graphical Models for sc-RNA seq Analysis
An archived version of the beachmat repository, see https://github.com/LTLA/beachmat for the active version.
Documentation how to run FASTGenomics analysis on a local machine for testing
Triple single cell analysis of microglia cell types for studying PIEZO1 alterations in Alzheimer patients
Single Cell guided Pangenome analysis pipeline using SPAdes, CheckM, GTDB-Tk, Prokka, Roary and extensive quality control.
Handlers and utilities for Contextualized analysis of single-cell datasets.
The package mixhvg uses mixture of highly variable gene selection methods to improve gene selection.
Trajectory inference method. It can decompose complex cell trajectories into interpretable transcriptional branching Gaussian processes.
Project for the course "Single Cell and Spatial Omics", held by prof. Tebaldi at UniTN, for the Master's degree in Quantitative and Computational Biology.
A model-based, unsupervised manifold learning method that factors complex cellular trajectories into interpretable bifurcating Gaussian processes of transcription.
Pipeline for the analysis of single-cell familial data from multiplex clonal assay
scMuffin - A MUlti-Features INtegrative approach for SC data analysis
Archived version of the zinbwave package. All future development will be done on https://github.com/drisso/zinbwave
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
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