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scVI
Deep generative modeling for single-cell transcriptomics
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Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
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VISION
A high-throughput and unbiased module for interpreting scRNA-seq data.
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BRAPeS
BCR reconstruction from short single cell RNA-seq
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MPRAnalyze
Analyse enhancer strength based on MPRA experiments.
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TRAPeS
TCR Reconstruction Algorithm for Paired-End Single cell
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scVI-data
datasets for scVI
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mpra_featurization
Featurizer for MPRA and other analyses. Can run DeepSea, Deepbind, epigenetic features, 5mer counts, Encode motif matrix, DNA shape, conservation, and some sequence features
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LineagePulse
Differential expression analysis for single-cell RNA-seq data
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FastProject
Dimensionality reduction for single cell RNA-seq data
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Rline
R wrapper around the LINE algorithm for network embedding
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condition_connectivity_problems
Algorithms for connectivity problems in condition-varying protein networks
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scRAD
Single-Cell Reproducibility Across Donors
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UMIpipe
A pipeline for processing UMI RNAseq data
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ImpulseDE
ImpulseDE
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dynamic_connectivity
Algorithms for connectivity problems in time-varying protein networks
