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acic23-competition

Data for and description of the ACIC 2023 data competition

adjustedcurves

An R-Package to estimate and plot confounder-adjusted survival curves (single event survival data) and confounder-adjusted cumulative incidence functions (data with competing risks) using various methods.

art046_nn_dcn_deep_convolutional_networks

Public repository containing materials used in the Deep Convolutional Neural Networks article

art047_nn_auto_encoder

Public repository containing materials used in the Undercomplete AutoEncoder article

atac-seq-pipeline

ENCODE ATAC-seq pipeline

awesome-neural-ode

A collection of resources regarding the interplay between differential equations, deep learning, dynamical systems, control and numerical methods.

ballgown

Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.

blast_plus_docs

bowtie2

A fast and sensitive gapped read aligner

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

codeclimate

Analyze code's readability (e.g., point out when a function is getting too long or even if the code is confusing in spots)

cookiecutter

A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

covid-19-rna-seq-datasets

A repository for sharing information on available COVID-19 RNA-Seq datasets

database_programming

SQL database, Cloudant NoSQL database, LeetCode materials

deep_omics

Repository for Short Course: Deep Learning in Omics

deephpms

Deep Hidden Physics Models: Deep Learning of Nonlinear Partial Differential Equations

deeplearningreview

A collaboratively written review paper on deep learning, genomics, and precision medicine

drgplotstats

An R package to plot and calculate statistics of payments by Diagnosis Related Group code.

exomiser

A Tool to Annotate and Prioritize Exome Variants

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

gatk

Official code repository for GATK versions 4 and up

genrich

Detecting sites of genomic enrichment

gseapy

Gene Set Enrichment Analysis in Python

harvard_bioinformatics_knowledgebase

This is the bioinformatics knowledgebase from Harvard Chan Bioinformatics Core

hdwgcna

High dimensional weighted gene co-expression network analysis

hello-codespaces

interestingr_programming

kagglecoding

laurae

Advanced High Performance Data Science Toolbox for R by Laurae