unitvelo
UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference
macrophage-regulation
Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
bd-lithium
A collection of source codes for network-based multi-omics analysis using integrated genome-wide association studies (GWAS) and transcriptomic data to identify genetic contribution into lithium response in patients with bipolar disorder (BD).
isocomp
Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq
rich_directrna
Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives
zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
tucca-rna-seq
Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects
tfactivity
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.