Bulk Rna Seq Python Packages

omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

openomicsbench

Traceable omics benchmarks with multi-method matrices, regression gates, portable bundles and sequence tools.

isoform-dominance

Is this functional isoform-class comparison measurable by short reads? Group-level identifiability, quantification and testing from bulk RNA-seq

txnova

A Python package with a Rust core that recovers unannotated spliced residual loci from bulk RNA-seq BAMs. CIGAR N junctions recurring in 2+ cohort samples and absent from the annotation become locus models. An optional control-vs-treat TPM screen flags treat-detected, control-silent loci. Output: residual catalog, optional contrast, and report.

pyomic

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

deconversation

DECONVersation is a tool designed for the deconvolution of bulk RNA-seq data using embeddings derived from large-scale, LLM-based foundation models. DECONVersation produces robust cell type proportions by leveraging these high-dimensional embeddings to eschew explicit marker selection and mitigate batch effects typically present in single-cell reference signature matrices.

iobrx

Bit-exact, multithreaded Python+Rust acceleration layer for IOBRpy — CIBERSORT, signature scoring, TPM, EPIC, quanTIseq, MCP-counter, ESTIMATE at 23–26× speed with bit-identical outputs

raptor-rnaseq

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.