crsky's repositories
scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
scikit-learn
scikit-learn: machine learning in Python
biopython
Official git repository for Biopython (originally converted from CVS)
EpiSCORE
Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
warp
WDL Analysis Research Pipelines
ggseg
Plotting tool for brain atlases, in ggplot
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
scgen
Single cell perturbation prediction
maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
pyranges
Performant Pythonic GenomicRanges
altair
Declarative statistical visualization library for Python
Python
All Algorithms implemented in Python
scanpy
Single-cell analysis in Python. Scales to >1M cells.
scGate
marker-based purification of cell types from single-cell RNA-seq datasets
tldr-python-client
Python command-line client for tldr pages
magic-python
Python 黑魔法手册
maxATAC
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
scFEA
single cell Flux Estimation Analysis (scFEA) Try the below web server!
muon
muon is a multimodal omics Python framework
fusca
Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it contains two modules: 1) CellRouter, for reconstruction of complex single-cell trajectories, and 2) CellComm, to infer intercellular communication networks from scRNA-seq data.
nichenetr
NicheNet: predict active ligand-target links between interacting cells
awesome-python
A curated list of awesome Python frameworks, libraries, software and resources
scDIOR
scDIOR: Single cell data IO softwaRe
GSEApy
Gene Set Enrichment Analysis in Python
cufflinks
Productivity Tools for Plotly + Pandas
DestVI-reproducibility
Reproducing the experiments of the DestVI paper
notebooks
Jupyter notebooks for the Natural Language Processing with Transformers book