#Rna-seq
Showing 26 of 26 repositories tagged #rna-seq, ranked by stars
๐งฌ gget enables efficient querying of genomic reference databases
๐ ๐ฃ ๐ฑ Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Tools to process and analyze deep sequencing data.
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
:snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
longcallR is a tool for SNP calling, haplotype phasing, and allele-specific analysis with long-read RNA-seq data.
Deep Learning based cell composition analysis with Scaden.
The START App: R Shiny Transcriptome Analysis Resource Tool
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
Transcriptomics Visualization R package.
This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.
๐ ๐ ๐ฏ๐จ๐ฅ๐ effortlessly translates differential expression datasets and RNAseq data into informative volcano plots. Highlight genes of interest with unprecedented ease. With just a single line of code, visualize complex datasets, gaining deeper insights and simplifying data representation
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
Iterative transfer learning with neural network improves clustering and cell type classification in single-cell RNA-seq analysis
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.
Immunology Informatics - Big Data Analysis in Immunology - Tutorials
A generative model for phenotypic-based drug discovery