3d-dna

3D de novo assembly (3D DNA) pipeline

adaptmt

Modifications to the adaptMT package including wrapper functions for XGBoost implementation with EM algorithm cross-validation tuning (see pre-print: https://www.biorxiv.org/content/early/2019/10/16/806471)

admixr

An R package for reproducible and automated ADMIXTOOLS analyses

admixtools

Tools test whether admixture occurred and more

al-folio

A beautiful, simple, clean, and responsive Jekyll theme for academics

alfda

ALFDA-Affinity based Local Fisher Discriminant Analysis

anatomogram

Anatomogram illustrating Expression Atlas experiments

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

argweaver

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

atlas

The Hugo boilerplate we use for our projects.

atlas_xx

automorph

vessel segmentation, artery and vein, optic disc, vascular feature analysis

awesome-chatgpt

A repository containing interesting demos / failure cases of ChatGPT

awesome-free-chatgpt

🆓免费的 ChatGPT 镜像网站列表，持续更新。List of free ChatGPT mirror sites, continuously updated.

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

bjfu.edu.qin_lab

bjfu.edu.qin_lab

bovine-graphs

Integrate multiple genome assemblies into a pangenome graph

card

caretplus

This is a modified version of caret: (Classification And Regression Training). An R package that contains misc functions for training and plotting classification and regression models. Credits go to the caret package where the below link shows the usage and how to compile your own model.

causaldiscoverytoolbox

Package for causal inference in graphs and in the pairwise settings. Tools for graph structure recovery and dependencies are included.

childhood_leukemia_single_cell_expression

cloudml

R interface to Google Cloud Machine Learning Engine

cmplot

📊 Circular and Rectangular Manhattan Plot

contig

This is the official implementation of the method ContIG, for self-supervised learning from medical imaging with genomics

coolbox

Jupyter notebook based genomic data visualization toolkit.

cv_duffyselection

cytoscape_workflows

collection of notebooks with different cytoscape workflows

d2l-en

Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 300 universities from 55 countries including Stanford, MIT, Harvard, and Cambridge.

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

da

DA incorporates the commonly used linear and non-linear, local and global supervised learning approaches (discriminant analysis). These discriminant analyses can be used to do ecological and evolutionary inference. We show the examples of demographic history inference, species identification, and population structure inference in the vignettes using the supervised discriminant analysis.