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cpgenie

ctdnatools

R package to work with ctDNA sequencing data

ctpsingle

deepcpg

Deep neural networks for predicting CpG methylation

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

delfi_scripts

dismir

dmatch

dnabert

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

edec

EDec (Epigenomic Deconvolution) is a technique that, starting from methylation and gene expression profiles of bulk tissue samples, infers cell type composition of each input sample as well as DNA methylation and gene transcription profiles of constituent cell types.

eforge

emerald

tools to efficiently retrieve and calculate LD

epigeneticclock

Calculate DNA methylation age using Horvath 2013 method

episcore

Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles

episomizer

Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data

faiss

A library for efficient similarity search and clustering of dense vectors.

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

flipflop

Python code to accompany our paper "Cell lineage tracing with molecular clocks based on fluctuating DNA methylation"

gadget_api

gene_lists

List of gene lists for genomic analyses.

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

hitrava

Convert your Huawei Health sport activities and import them in Strava.

hms-health-demo-java

HMS Health demo code provides demo programs for your reference or usage. Developers can access the Huawei Health Platform and obtain sports & health data by integrating HUAWEI Health.

iheatmapr

Complex, interactive heatmaps in R

informme

An information-theoretic pipeline for methylation analysis of WGBS data

introgression-detection

jabba

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

kallisto-scatac