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libsdae-autoencoder-tensorflow

A simple Tensorflow based library for Deep autoencoder and denoising AE.

lineagetreebuilder

linearpartition

Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities

ludwig

Ludwig is a toolbox built on top of TensorFlow that allows to train and test deep learning models without the need to write code.

lungcancer_sv_timing_analyses

mcrcs

meth-report-generator

甲基化报告自动化

meth_atlas

methtuple

methtuple is a methylation caller for methylation events that co-occur on the same DNA fragment from high-throughput bisulfite sequencing data, such as methylC-seq.

mgatk

mgatk: mitochondrial genome analysis toolkit

mocha

MOsaic CHromosomal Alterations (MoChA) caller

msisensor-ct

Microsatellite instability (MSI) detection for cfDNA samples.

mutationtimer

An R package to time somatic mutations

neutral-tumour-evolution

oneliners

Useful bash one-liners for bioinformatics.

oscilloscopetools

Small utilities in Perl and R to save, process, and plot oscilloscope data

palimpsest

An R package for studying mutational and structural variant signatures along clonal evolution in cancer.

pames

Tool to estimate purity of tumor samples exploiting DNA Methylation data

pcam

The PatchCamelyon (PCam) deep learning classification benchmark.

pcgr

Personal Cancer Genome Reporter (PCGR)

pfastq-dump

parallel-fastq-dump implementation in bash script

phial

Precision Heuristics for Interpreting the Alteration Landscape

phyc

Clustering cancer evolutionary trees

phylogicndt

phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

psap-pipeline

pyloh

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

rck

RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes

revolver

REVOLVER - Repeated Evolution in Cancer