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2020_wilk_covid

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

abis

academic_writing

academic writing

adam

Adaptive Daisy Model to discriminate core-fitness/context-specific essential genes in large scale CRISPR-Cas9 screens

aneuploidy_dependencies

scripts for plots

autogenes

awesome-community-detection

A curated list of community detection research papers with implementations.

awesome-deep-learning-single-cell-papers

awesome-foundation-models-in-medical-imaging

A curated list of foundation models for vision and language tasks in medical imaging

awesome-graph-classification

A collection of important graph embedding, classification and representation learning papers with implementations.

awesome-information-bottleneck

This is a curated list for Information Bottleneck Principle, in memory of Professor Naftali Tishby.

awesome-interpretable-machine-learning

awesome-kan

A comprehensive collection of KAN(Kolmogorov-Arnold Network)-related resources, including libraries, projects, tutorials, papers, and more, for researchers and developers in the Kolmogorov-Arnold Network field.

awesome-machine-learning-interpretability

A curated list of awesome machine learning interpretability resources.

awesome-mim-1

Awesome List of Masked Image Modeling (MIM) Papers for Self-supervised Visual Representation Learning

awesome-multi-omics

List of software packages for multi-omics analysis

awesome-scalability

The Patterns of Scalable, Reliable, and Performant Large-Scale Systems

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bayestme

BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data

benchmarking_variant_callers

In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We evaluate the performances of these tools in different read depths, genomic contexts, functional regions and variant allele frequencies.

biological-network-analysis-review

collection of biological network analysis methods

biotools

A list of useful bioinformatics resources

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

bisque

An R toolkit for estimation of cell composition from bulk expression data

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

book

bulk-rna-seq-review

collections of bulk rna-seq papers

cancer-subtype-clustering

collections of cancer subtype clustering methods

ccle_heterogeneity

cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data