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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

ascets

This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm-level copy-number variant calls and arm-level weighted average log2 segment means from segmented copy number data.

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

geomxtools

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.

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