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
CELLECT
CELLECT is a computational toolkit for identifing likely etiologic cell-types underlying complex traits.
CELLEX
CELLEX is a tool for computing cell-type expression specificity profiles.
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).
IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences
IsoformSwitchAnalyzeR software
SatuRn
Statistical method for analysis for differential transcript usage (DTU) from full-length single cell data.
SHARP
An ensemble random projection-based algorithm that is scalable to clustering up 10 million single cell transcriptomes.
TENET
Predicts large-scale gene regulatory cascades/relationships from scRNAseq data.
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.