Pinned Repositories
admin-training
Galaxy Admin Training
ags_conda_recipes
A tutorial (+ build recipes) describing how to use conda for C, C++, and python package management
Aperture
Alignment-free detection of structural variations and viral integrations in circulating tumor DNA
apt.oncoscan.2.4.0
Affymetrix OncoScan / OncoScan_CNV processing using apt-copynumber-onco-ssa (2.4.0)
argparse2tool
transparently build CWL and Galaxy XML tool definitions for any script that uses argparse
Arima-SV-Pipeline
arriba
Fast and accurate gene fusion detection from RNA-Seq data
ascat
ASCAT copy number R package
ascatNgs
Somatic copy number analysis using WGS paired end wholegenome sequencing
nvk747's Repositories
nvk747/admin-training
Galaxy Admin Training
nvk747/Aperture
Alignment-free detection of structural variations and viral integrations in circulating tumor DNA
nvk747/Arima-SV-Pipeline
nvk747/arriba
Fast and accurate gene fusion detection from RNA-Seq data
nvk747/ascat
ASCAT copy number R package
nvk747/CaSpER
nvk747/CICERO
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
nvk747/cnvkit
Copy number variant detection from targeted DNA sequencing
nvk747/CopyNumber_Oncoscan
Data processing and analysis of genomic copy number data
nvk747/countToFPKM
Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
nvk747/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
nvk747/delfi_scripts
nvk747/docker-galaxy-stable
:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
nvk747/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
nvk747/EaCoN
Easy Copy Number !
nvk747/Edit_Efficiency_Correction
Project of Wang Lab in IBMS: Identification of LOF variants using base editing screens with editing efficiency correction
nvk747/FRASER
nvk747/FuSeq_WES
nvk747/galaxy_papaa
This repository is for installing and running a docker galaxy instance with pancancer aberrant pathway activity analysis (PAPAA) tools
nvk747/ovaHRDscar
R package to quantify allelic imbalances associated with homologous recombination deficiency in ovarian cancer. Use as input a list of segments per samples as those generated by ASCAT.
nvk747/papaa
nvk747/RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
nvk747/reproduce_liver_final
Code to reproduce "Detecting liver cancer using cell-free DNA fragmentomes
nvk747/RNApeg
RNA junction finder
nvk747/ScanITD
A python tool to detect internal tandem duplication with robust variant allele frequency estimation
nvk747/shallowHRD
This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
nvk747/Squirls
Interpretable prioritization of splice variants in diagnostic next-generation sequencing
nvk747/tools-iuc
Tool Shed repositories maintained by the Intergalactic Utilities Commission
nvk747/training-material
A collection of Galaxy-related training material
nvk747/warp
WDL Analysis Research Pipelines