Transcriptome Python Packages

wormneuroatlas

Neural signal propagation atlas (Randi et al.), genome (WormBase), single-cell transcriptome (Taylor et al.), neuropeptide/GPCR deorphanization (Beets et al.), monoaminergic connectome (Bentley et al.), and chemical-synapse sign predictions (Fenyves et al.) all in one place. Read the docs: https://francescorandi.github.io/wormneuroatlas/

isoquant

A universal toolkit for upstream processing of long RNA reads

mavis

Merging, Annotation, Validation, and Illustration of Structural variants

garnet

No description available

disc

A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

eastr

Emending Alignment of Spliced Transcript Reads

isocon

Derives consensus sequences from a set of long noisy reads by clustering and error correction.

isonclust

De novo clustering of long transcript reads into genes

swan-vis

A Python library to visualize and analyze long-read transcriptomes

orthomap

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.