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rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rocker-versioned

Run current & prior versions of R using docker

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rtscars

sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

sciclone

An R package for inferring the subclonal architecture of tumors

scimpute

Accurate and robust imputation of scRNA-seq data

scmut

sctda

An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data

seqlib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

signature.tools.lib

R package containing useful functions for mutational signature analysis

sigprofilersimulator

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

singlecellglioma-verhaaklab

smc-het-challenge

Development of the automated scoring system for the SMC-Het Challenge

snakemake_nextflow_wdl

simple comparison of snakemake, nextflow and cromwell/wdl

speedseq

A flexible framework for rapid genome analysis and interpretation

subclonalselection.jl

Inferring selection in cancer sequencing data using ABC and population based simulations

sumnerdocs

Sumner HPC Documentation - Beta and Unofficial!

svclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.

svetect

A tool for identifying and classifying structural rearrangements and chromoplexy from high throughput sequencing data.

telomeasure

Telomeasure estimates average telomere length from whole genome sequencing (WGS) BAM files.

telseq

A software for calculating telomere length

treeshapedrearrangements

Code and data from Koche et al. (under review)

treeshapedrearrangementsshinyapp

A Shiny app that visualizes the data from Koche et al. (under review).

triagen

Triaging of genetic variants in cancer

tumor-subclonal-reconstruction

Winning model of DREAM SMC-Het Challenge for characterizing intra-tumor heterogeneity by using genomic variation data

tumortype-wgs

Classifying tumor types based on Whole Genome Sequencing (WGS) data

valibam

Minimal nextflow pipeline to check integrity of BAM files with various tools and to generate the checksum (md5) of each files.

watershed

Prioritization of functional rare genetic variants by integrating genomic annotations and RNA-seq

wdlrunr

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources