Next Tools

Next Tools

Some notes describing interesting tools that raised our attention and could be implemented in the future. It can also be seen as a way to keep track of interesting stuff discussed in any platform (Gitter, Slack, ...). It's also a way to keep the GitHub issues clean.

Cell Type Annotation

Papers

1. A comparison of automatic cell identification methods for single-cell RNA sequencing data
   • Url: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1795-z
   • Code: https://github.com/tabdelaal/scRNAseq_Benchmark

Tools

• OnClass
  • Paper: https://www.biorxiv.org/content/10.1101/810234v1
  • GitHub: https://github.com/wangshenguiuc/OnClass
  • Docs: https://onclass.readthedocs.io/en/latest/
• SVM_rejection
  • Code: https://github.com/tabdelaal/scRNAseq_Benchmark/blob/master/Scripts/run_SVM_rejection.py
  • Paper Ref.: 1.
  • Notes:
    • Ranked as the best performer in the paper
• Garnett
  • Docs: https://cole-trapnell-lab.github.io/garnett/docs/
• CellTypeScan
  • Docs: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/blob/develop/CellTypeScan.md
• CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature.
  • GitHub: https://github.com/shunfumao/cellmesh
  • Paper: https://www.biorxiv.org/content/10.1101/2020.05.29.124743v1

Batch Effect Correction/Data Integration

Papers

• https://www.biorxiv.org/content/10.1101/2020.05.22.111161v1

Tutorials

• https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/scanpy/scanpy_03_integration.html

Tools

• DESC
  • GitHub: https://github.com/eleozzr/desc
  • Paper: https://www.nature.com/articles/s41467-020-15851-3
  • Notes: better than Harmony ? => to implement ?!
• Liger
  • GitHub: https://github.com/MacoskoLab/liger
  • Paper: https://www.cell.com/cell/fulltext/S0092-8674%2819%2930504-5
• Seurat CCA (v2)
• Seurat Anchors (v3)
• Scanorama:
  • GitHub: https://github.com/brianhie/scanorama
  • Paper: https://www.nature.com/articles/s41587-019-0113-3
• BatchBench - Nextflow workflow for running the following scRNA-Seq data batch effect correction methods
  • GitHub: https://github.com/cellgeni/batchbench
  • Paper: https://www.biorxiv.org/content/10.1101/2020.05.22.111211v2.full.pdf

Clustering

Tools

• SCAAF
  • GitHub: https://github.com/SCCAF/sccaf
• TooManyCells
  • Paper: https://www.nature.com/articles/s41592-020-0748-5
  • GitHub: https://github.com/GregorySchwartz/too-many-cells
• GiniClust3
  • Description: a fast and memory-efficient tool for rare cell type identification
  • bioRXiv: https://www.biorxiv.org/content/10.1101/788554v1
  • GitHub: https://github.com/rdong08/GiniClust3
  • Docs: https://giniclust3.readthedocs.io/en/latest/tutorials/
• hicat
  • Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985242/
  • GitHub: https://github.com/AllenInstitute/scrattch.hicat
  • Docs:
    • https://taxonomy.shinyapps.io/scrattch_tutorial/
    • http://htmlpreview.github.io/?https://github.com/AllenInstitute/scrattch.hicat/blob/master/vignettes/scrattch.hicat_release.html
• scNSBM - An interface for Nested Stochastic Block Model for single cell analysis
  • Paper: Coming...
  • GitHub: https://github.com/dawe/scNSBM

Visualization

Tools

• openTSNE
  • Description: openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor Embedding (t-SNE) [1], a popular dimensionality-reduction algorithm for visualizing high-dimensional data sets. openTSNE incorporates the latest improvements to the t-SNE algorithm, including the ability to add new data points to existing embeddings [2], massive speed improvements [3] [4], enabling t-SNE to scale to millions of data points and various tricks to improve global alignment of the resulting visualizations.
  • GitHub: https://github.com/pavlin-policar/openTSNE
  • Notes:
    • Possible to change the initialization
• densvis
  • Description: Density-preserving data visualization tools den-SNE and densMAP
  • Paper: https://www.nature.com/articles/s41587-020-00801-7
  • GitHub: https://github.com/hhcho/densvis

Misc

• https://jlmelville.github.io/smallvis/init.html
• https://github.com/dkobak/tsne-umap-init/blob/master/tsne-umap-circle.ipynb
• https://github.com/linqiaozhi/DR_benchmark_initialization

Differential expression

Tools

• genesorteR - Feature Ranking for Single Cell Data
  • Paper: https://www.biorxiv.org/content/10.1101/676379v2.full
  • GitHub: https://github.com/mahmoudibrahim/genesorteR
• muscat
  • GitHub: https://github.com/HelenaLC/muscat
  • Paper: https://www.nature.com/articles/s41467-020-19894-4

Quality Controls/Filtering

Papers

Tools

• dropkick
  • Description: Automated cell filtering for single-cell RNA sequencing data
  • Paper: https://www.biorxiv.org/content/10.1101/2020.10.08.332288v1?rss=1
  • GitHub: https://github.com/KenLauLab/dropkick
  • Docs: https://github.com/KenLauLab/dropkick/blob/master/dropkick_tutorial.ipynb
• CellBender remove-background
  • Description: software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  • GitHub: https://github.com/broadinstitute/CellBender
• SoupX
  • GitHub: https://github.com/constantAmateur/SoupX
  • bioRXiv: https://www.biorxiv.org/content/10.1101/303727v2
• DecontX
  • GitHub: https://github.com/campbio/celda
  • Paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1950-6
• PhantomPurgeR
  • Description: R package for the optimal purging of phantom molecules by the robust estimation of the sample index hopping rate in multiplexed droplet-based single-cell RNA-seq data
  • Paper: https://www.nature.com/articles/s41467-020-16522-z
  • GitHub: https://github.com/csglab/PhantomPurgeR
  • bioRXiv: https://www.biorxiv.org/content/10.1101/617225v5
• ROGUE
  • Description: Ratio of Global Unshifted Entropy
  • Paper: https://github.com/PaulingLiu/ROGUE
  • GitHub: https://www.nature.com/articles/s41467-020-16904-3
• scds - single cell doublet scoring
  • Description: In-silico doublet annotation for single cell RNA sequencing data
  • GitHub: https://github.com/kostkalab/scds
  • Paper: https://academic.oup.com/bioinformatics/article/36/4/1150/5566507
• scDblFinder
  • GitHub: https://github.com/plger/scDblFinder
• DoubletDecon
  • Description: Deconvoluting doublets from single-cell RNA-sequencing data
  • GitHub: https://github.com/EDePasquale/DoubletDecon
• DoubletFinder
  • GitHub: https://github.com/chris-mcginnis-ucsf/DoubletFinder
• Solo
  • Description: Doublet detection via semi-supervised deep learning
  • GitHub: https://github.com/calico/solo
• Scrublet
  • Description: Single-Cell Remover of Doublets
  • Paper: https://www.sciencedirect.com/science/article/pii/S2405471218304745
  • GitHub: https://github.com/swolock/scrublet, https://github.com/AllonKleinLab/scrublet

Mapping & Counting

Tools

• zUMIs
  • GitHub: https://github.com/sdparekh/zUMIs
  • Paper: https://doi.org/10.1093/gigascience/giy059

Enrichment

Tools

• iDEA
  • Paper: https://www.nature.com/articles/s41467-020-15298-6
  • GitHub: https://github.com/xzhoulab/iDEA

Feature Prioritization

Tools

• SPECS
  • Description: Python script to for a non-parametric specificity score that is compatible with unequal sample group sizes
  • GitHub: https://github.com/celineeveraert/SPECS
• scRFE
  • Description: Single-cell identity definition using random forests and recursive feature elimination. scRFE is a Python package that uses a one versus all random forest classifier with recursive feature elimination to identify the set of genes necessary and sufficient to describe the different features of your single-cell RNA sequencing data.
  • GitHub: https://github.com/czbiohub/scRFE
  • Docs: https://scrfe.readthedocs.io/en/latest/index.html

Trajectory Inference

Tools

• VeTra: a new trajectory inference tool based on RNA velocity
  • Paper: https://www.biorxiv.org/content/10.1101/2020.09.01.277095v1
  • GitHub: https://github.com/wgzgithub/VeTra

Conversion

Tools

• sceasy
  • GitHub: https://github.com/cellgeni/sceasy
• Zellkonverter
  • GitHub: https://github.com/theislab/zellkonverter

Miscellaneous

Tools

• pipeComp
  • GitHub: https://github.com/plger/pipeComp
  • Paper: https://www.biorxiv.org/content/10.1101/2020.02.02.930578v2.full.pdf
• geosketch
  • GitHub: https://github.com/brianhie/geosketch
  • Paper: https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30152-8
• opt-tSNE
  • GitHub: https://github.com/omiq-ai/Multicore-opt-SNE
  • Paper: https://www.nature.com/articles/s41467-019-13055-y

Scripts

• https://github.com/maehrlab/thymusatlastools/blob/master/R/exploratory_pipeline.Rmd