Modern scRNA-seq analysis tools in a single pipeline
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Updated
Jul 15, 2022 - R
Modern scRNA-seq analysis tools in a single pipeline
Permutation testing in single cell analysis
Infer and visualize cell-cell communication for single-cell RNA-seq data
An example of immunopipe
TRIAGE is provided here as an R package comprised of three tools: 1) TRIAGEgene, 2) TRIAGEcluster, and 3) TRIAGEparser, along with a set of functions that streamlines creation of publication-ready figures and facilitates smoother data analysis.
diabetes
scripts for scRNA-Seq/scATAC-Seq
Shiny web app builder for single-cell data
Analysis of Single-Cell RNA data from SRR14294834 in peripheral blood mononuclear cells in severe asthma
Prediction of surface protein expression from mRNA expression using a regression auto-encoder neural network.
Nek2 single cell analysis
This project employs Scanpy in Python for analyzing spatial transcriptomics data, encompassing preprocessing, quality control, clustering, and marker gene identification, resulting in informative visualizations to reveal gene expression patterns and cellular interactions within tissue samples.
Biological prior guided RNA kinetics inference
A collection of 49 simulation methods for single-cell and spatial transcriptome data
All analysis performed during the generation of the manuscript "ICAT: A Novel Algorithm to Robustly Identify Cell States Following Perturbations in Single Cell Transcriptomes"
scMLnet2.0: Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
SBC analysis with DIGIST (In progress)
Common functions used in data simulation and evaluation
Single cell Perturbations - Analysis of Differential gene Expression
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