Manage analysis tools available in ASAP.
| Name | Label | Package | Tool Type | Title | |
|---|---|---|---|---|---|
| MulticoreTSNE | MulticoreTSNE | R | Multicore modification of Barnes-Hut t-SNE | Show | |
| AnnData | anndata | Python | Annotated data matrices for single-cell analysis | Show | |
| bit64 | bit64 | R | A S3 Class for Vectors of 64bit Integers. | Show | |
| Cairo | Cairo | R | R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output. | Show | |
| Silhouette Plot [cluster package] | cluster | R | "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. | Show | |
| ComBat [sva package] | sva | R | Surrogate Variable Analysis | Show | |
| data.table | data.table | R | Extension of 'data.frame' | Show | |
| DESeq2 | DESeq2 | R | Differential gene expression analysis based on the negative binomial distribution | Show | |
| devtools | devtools | R | Tools to Make Developing R Packages Easier. | Show | |
| edgeR | edgeR | R | Empirical Analysis of Digital Gene Expression Data in R | Show | |
|
ensembl
|
Ensembl | — | Database | — | Show |
| Ensembl genomes | — | Database | Ensembl database for non-vertebrate species | Show | |
| Ensembl vertebrates | — | Database | Ensembl database for vertebrates | Show | |
|
fbbt
|
Flybase Anatomy Ontology | — | Database | — | Show |
| flexmix | flexmix | R | Flexible Mixture Modeling. | Show | |
| future.apply | future.apply | R | Apply Function to Elements in Parallel using Futures. | Show | |
| Gene Atlas | — | Database | — | Show | |
| genefilter | genefilter | R | Methods for filtering genes from high-throughput experiments | Show | |
| Gene Ontology | — | Database | — | Show | |
| GPy | g | Python | Gaussian Process framework | Show | |
| MSigDB from GSEA | — | Database | — | Show | |
| h5py | h5py | Python | HDF5 for Python | Show | |
|
hcao
|
Human Cell Atlas Ontology | — | Database | — | Show |
| hdf5r | hdf5r | R | Interface to the 'HDF5' Binary Data Format. | Show | |
| Java JDK | java | Java | — | Show | |
| JSC [Java statistical API] | — | Java | — | Show | |
| jsonlite | jsonlite | R | A Simple and Robust JSON Parser and Generator for R. | Show | |
| KEGG | — | Database | — | Show | |
| KernSmooth | KernSmooth | R | Functions for Kernel Smoothing Supporting Wand & Jones (1995). | Show | |
| leidenalg | leidenalg | Python | Leiden algorithm | Show | |
| limix | limix | Python | — | Show | |
| Limma / Voom | limma | R | Linear Models for Microarray Data | Show | |
| loompy | loompy | Python | Manipulation of Loom files in Python | Show | |
| louvain | louvain | Python | Community detection in large networks | Show | |
| M3Drop | M3Drop | R | Michaelis-Menten Modelling of Dropouts in single-cell RNASeq. | Show | |
| MAST | MAST | R | Model-based Analysis of Single Cell Transcriptomics. | Show | |
| matplotlib | matplotlib | Python | Visualization with Python | Show | |
| Matrix | Matrix | R | Sparse and Dense Matrix Classes and Methods. | Show | |
| MDS [MASS Package] | MASS | R | Support Functions and Datasets for Venables and Ripley's MASS | Show | |
| nlme | nlme | R | Linear and Nonlinear Mixed Effects Models | Show | |
| numba | numba | Python | Accelerate Python Functions | Show | |
| numpy | numpy | Python | The fundamental package for scientific computing with Python | Show | |
| Pagoda / SCDE | scde | R | Single Cell Differential Expression | Show | |
| PAM / Silhouette Plot [cluster package] | cluster | R | "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. | Show | |
| pandas | pandas | Python | Data analysis and manipulation tool | Show | |
| PanglaoDB | — | Database | PanglaoDB | Show | |
| Plotly | plotly | R | Create Interactive Web Graphics via 'plotly.js'. | Show | |
| PyDESeq2 | pydeseq2 | Python | Differential expression analysis in Python (DESeq2 reimplementation) | Show | |
| pylab | pylab | Python | — | Show | |
| Python | python | Python | — | Show | |
| Python3 | python3 | Python | — | Show | |
|
r
|
R | R | R | R | Show |
| R6 | R6 | R | Encapsulated Classes with Reference Semantics. | Show | |
| reticulate | reticulate | R | Interface to 'Python'. Interface to 'Python' modules, classes, and functions. | Show | |
| rhdf5 | rhdf5 | R | R Interface to HDF5. | Show | |
| Rtsne | Rtsne | R | T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation. | Show | |
| sanon | sanon | R | Stratified Analysis with Nonparametric Covariable Adjustment. | Show | |
| SC3 | SC3 | R | Single-Cell Consensus Clustering | Show | |
| SCAN / UPC | SCAN.UPC | R | Single-channel array normalization (SCAN) and Universal exPression Codes (UPC) | Show | |
| Scanpy | scanpy | Python | Single-Cell Analysis in Python | Show | |
| scater | scater | R | Single-Cell Analysis Toolkit for Gene Expression Data in R. | Show | |
| scikit.learn | scikit-learn | Python | Machine Learning in Python | Show | |
| scipy | scipy | Python | Fundamental algorithms for scientific computing in Python | Show | |
|
sclvm
|
scLVM | scLVM | R | — | Show |
| scran | scran | R | Methods for Single-Cell RNA-Seq Data Analysis. | Show | |
| Scrublet | scrublet | Python | Single-cell doublet detection | Show | |
| Seurat | Seurat | R | Tools for Single Cell Genomics. | Show | |
| statmod | statmod | R | Statistical Modeling. | Show | |
| R version & default packages [stats] (K-means, PCA, Hierarchical clustering, distance, correlation) | stats | R | — | Show | |
| UMAP | umap-learn | Python | Uniform Manifold Approximation and Projection for Dimension Reduction | Show | |
| XVector | XVector | R | Foundation of external vector representation and manipulation in Bioconductor. | Show | |
| ZIFA | ZIFA | Python | Zero-inflated dimensionality reduction algorithm for single-cell data. | Show |