Software

Atlas-scale regulatory network inference framework

Atlas-scale regulatory network inference framework paper

Atlas-scale regulatory network inference framework software

Cacoa

Case-Control Analysis: the package allows comprehensive cross-condition analysis, e.g. healthy vs disease

Cacoa software

CELLECT

CELLECT is a computational toolkit for identifing likely etiologic cell-types underlying complex traits.

CELLECT paper

CELLECT software

CELLEX

CELLEX is a tool for computing cell-type expression specificity profiles.

CELLEX paper

CELLEX software

Conos

Clustering on network of samples. Integration of single cell data (any modality, from transcriptomics to proteomics). Performs pairwise alignments of individual samples, identifying plausible inter-sample cell–cell correspondence (inter-sample edges).

Conos paper

Conos software

IsoformSwitchAnalyzeR

Identify, Annotate and Visualize Isoform Switches with Functional Consequences

IsoformSwitchAnalyzeR paper

IsoformSwitchAnalyzeR software

SatuRn

Statistical method for analysis for differential transcript usage (DTU) from full-length single cell data.

SatuRn paper

SatuRn software

SHARP

An ensemble random projection-based algorithm that is scalable to clustering up 10 million single cell transcriptomes.

SHARP paper

SHARP software

TENET

Predicts large-scale gene regulatory cascades/relationships from scRNAseq data.

TENET paper

TENET software

VeTra

A tool to infer the trajectories from scRNAseq data. Uniquely, VeTra can perform grouping of cells that are in the same stream of trajectory.

VeTra paper

VeTra software