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r-gpgr
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public |
Genomics Platform Group Reporting
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2024-08-20 |
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r-rportal
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public |
UMCCR data portal R functionality
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2024-08-14 |
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r-dracarys
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public |
DRAGEN workflow post-processing
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2024-08-14 |
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r-rnasum
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public |
RNAseq-based cancer patient reports
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2024-07-04 |
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r-cpsr
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public |
Cancer Predisposition Sequencing Reporter
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2024-06-26 |
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pcgr
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public |
None
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2024-06-14 |
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r-pcgrr
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public |
Personal Cancer Genome ReporteR. Functions, tools and utilities for the generation of clinical cancer genome reports with PCGR. This R package is an integrated part of the Docker/Conda-based PCGR workflow (https://github.com/sigven/pcgr), it should thus not be used as a stand-alone package.
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2024-06-10 |
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r-rnasum.data
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public |
Reference data for RNAsum
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2024-05-16 |
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r-cttsor
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public |
cttso-related R functionality
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2024-03-25 |
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r-manhattanly
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public |
Create interactive manhattan, Q-Q and volcano plots that are usable from the R console, in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
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2023-11-16 |
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r-woofr
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public |
Helper R Functions for woof (https://github.com/pdiakumis/woof).
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2023-09-25 |
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vcfanno
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public |
annotate a VCF with other VCFs/BEDs/tabixed files
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2023-09-14 |
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oviraptor
|
public |
Oncoviral integration in cancer whole genome data
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2023-09-04 |
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multiqc
|
public |
Create aggregate bioinformatics analysis reports across many samples and tools
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2023-08-14 |
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r-sigrap
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public |
Wrappers for somatic mutation signature analysis tools
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2023-07-12 |
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r-signature.tools.lib
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public |
R package with useful functions for mutational signatures analysis.
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2023-07-12 |
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r-chord
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public |
CHORD is a random forest model that uses the relative counts of somatic mutation contexts to predict homologous recombination deficiency (HRD). The primary contexts used by CHORD are deletions with flanking microhomology and 1-100kb structural duplications. Additionally, 1-100kb structural duplications are used to distinguish BRCA1-type HRD from BRCA2-type HRD.
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2023-07-12 |
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r-nnlm
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public |
This is a package for Non-Negative Linear Models (NNLM). It implements fast sequential coordinate descent algorithms for non-negative linear regression and non-negative matrix factorization (NMF). It supports mean square error and Kullback-Leibler divergence loss. Many other features are also implemented, including missing value imputation, domain knowledge integration, designable W and H matrices and multiple forms of regularizations.
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2023-07-12 |
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r-mutsigextractor
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public |
Extracts SNV, indel, DBS, and SV signatures from vcf files.
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2023-07-12 |
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vcf2maf
|
public |
Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms
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2023-06-18 |
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lndir
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public |
No Summary
|
2023-06-18 |
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compar
|
public |
No Summary
|
2023-06-18 |
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umccr_refdata
|
public |
UMCCR reference data API
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2023-06-18 |
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pyvcf
|
public |
Variant Call Format (VCF) parser for Python
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2023-06-18 |
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woof
|
public |
Compare genomic data from two sources
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2023-06-18 |
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r-activedriverwgs
|
public |
A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data. The method is part of the following publication: Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Molecular Cell (2020) <doi:10.1016/j.molcel.2019.12.027>.
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2023-06-16 |
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fqtools
|
public |
An efficient FASTQ manipulation suite.
|
2023-06-16 |
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woof-nf
|
public |
No Summary
|
2023-06-16 |
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tsvtools
|
public |
Utilities for operating with tab-separated files: viewing, filtering, reordering
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2023-06-16 |
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ngs_utils
|
public |
Python utilities for bioinformatics tools and pipelines
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2023-06-16 |
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r-pebbles
|
public |
Contains cancer genomics datasets for running tests and examples in the rock R package (https://github.com/pdiakumis/rock).
|
2023-06-16 |
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versionpy
|
public |
Small utility to track and bump the version of your python tool
|
2023-06-16 |
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r-rock
|
public |
Contains visualisation functions for bioinformatics work at UMCCR.
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2023-06-16 |
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tsvfmt
|
public |
Tab-separated file viewer for command line
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2023-06-16 |
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reference_data
|
public |
Versioning of reference data used in UMCCR pipelines, and python API to access it
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2023-06-16 |
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bed_annotation
|
public |
Genome capture target coverage evaluation tool
|
2023-06-16 |
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vcf_stuff
|
public |
Evaluating, filtering, comparing, and visualising variant calls
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2023-06-16 |
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r-mailr
|
public |
Interface to Apache Commons Email to send emails from R.
|
2023-06-16 |
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r-h2o
|
public |
R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models, Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Cox Proportional Hazards, K-Means, PCA, Word2Vec, as well as a fully automatic machine learning algorithm (AutoML).
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2023-06-16 |
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r-googlesheets
|
public |
Interact with Google Sheets from R.
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2023-06-16 |
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r-dndscv
|
public |
This package contains functions for studying selection on coding sequences using a Poisson implementation of dN/dS. A Poisson model of dN/dS facilitates the study of selection beyond traditional codon models, including complex context-dependent mutation effects and selection on nonsense and splice site mutations. This model is best suited for resequencing studies, with very low density of mutations per base pair. The model was initially developed for cancer genome sequencing studies, and specific functions are provided to perform driver gene discovery using the dNdScv method on human cancer genomic data. The first beta version of this package only supports analyses of human data. Future versions of the package will support analyses on any species using a general FASTA input format.
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2023-06-16 |
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r-beepr
|
public |
The main function of this package is beep(), with the purpose to make it easy to play notification sounds on whatever platform you are on. It is intended to be useful, for example, if you are running a long analysis in the background and want to know when it is ready.
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2023-06-16 |
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r-lares
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public |
R library for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, such as Machine Learning, Data Wrangling, Exploratory, and Scrapper, lares helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or extensive programming skills.
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2023-06-16 |
