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)
tucca-rna-seq
Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects
zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
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).
rich_directrna
Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives
isocomp
Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq
tfactivity
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.