sigminer - Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

Last updated 2 months ago

bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualization

137 stars 4.95 score 92 dependencies 2 dependents

UCSCXenaShiny - Interactive Analysis of UCSC Xena Data

Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.

Last updated 2 days ago

cancer-datasetshiny-appsucsc-xena

83 stars 4.42 score 111 dependencies

UCSCXenaShiny - Interactive Analysis of UCSC Xena Data

Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.

Last updated 2 days ago

cancer-datasetshiny-appsucsc-xena

83 stars 4.42 score 111 dependencies

UCSCXenaTools - Download and Explore Datasets from UCSC Xena Data Hubs

Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.

Last updated 7 months ago

api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena

100 stars 4.38 score 35 dependencies 1 dependents

UCSCXenaTools - Download and Explore Datasets from UCSC Xena Data Hubs

Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.

Last updated 7 months ago

api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena

100 stars 4.38 score 35 dependencies 1 dependents

ezcox - Easily Process a Batch of Cox Models

A tool to operate a batch of univariate or multivariate Cox models and return tidy result.

Last updated 7 months ago

batch-processingcox-model

20 stars 2.69 score 40 dependencies 1 dependents

DoAbsolute - Automate Absolute Copy Number Calling

Provide an easy interface to automate estimation of absolute copy number, purity, ploidy using 'ABSOLUTE'.

Last updated 8 months ago

absolutecopy-number-variationfirehose

35 stars 2.46 score 5 dependencies

phylotaR - Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

Last updated 8 days ago

blastngenbankpeer-reviewedphylogeneticssequence-alignment

23 stars 2.14 score 69 dependencies

gcap - Gene-level Circular Amplicon Prediction

Provides data processing pipeline feeding paired bam files (or allele-specific copy number data) and XGBOOST model for predicting tumor circular amplicons (also known as ecDNA) in gene level.

Last updated 2 months ago

ecdnapipelinetumor-genomicswesxgboost

14 stars 2.00 score 118 dependencies

contribution - A Tiny Contribution Table Generator Based on 'ggplot2'

Contribution table for credit assignment based on 'ggplot2'. This can improve the author contribution information in academic journals and personal CV.

Last updated 2 years ago

contributioncreditggplot2research

10 stars 1.46 score 46 dependencies

tinyscholar - Get and Show Personal 'Google Scholar' Profile

Provides functions to get personal 'Google Scholar' profile data from web API and show it in table or figure format.

Last updated 7 months ago

google-scholar

8 stars 1.46 score 77 dependencies

contribution - A Tiny Contribution Table Generator Based on 'ggplot2'

Contribution table for credit assignment based on 'ggplot2'. This can improve the author contribution information in academic journals and personal CV.

Last updated 2 years ago

contributioncreditggplot2research

10 stars 1.46 score 46 dependencies

ggpolar - Dots and Their Connections in Polar Coordinate System

Provides basic graphing functions to fully demonstrate point-to-point connections in a polar coordinate space.

Last updated 2 years ago

ggplot2-enhancements

9 stars 1.40 score 28 dependencies

copynumber - Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

Last updated 1 years ago

14 stars 1.38 score 17 dependencies

cellscape - Explores single cell copy number profiles in the context of a single cell tree

CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.

Last updated 3 months ago

bioconductor-package

1.31 score 44 dependencies

regport - Regression Model Processing Port

Provides R6 classes, methods and utilities to construct, analyze, summarize, and visualize regression models.

Last updated 2 years ago

batch-processingregression-models

6 stars 1.18 score 48 dependencies

metawho - Meta-Analytical Implementation to Identify Who Benefits Most from Treatments

A tool for implementing so called 'deft' approach (see Fisher, David J., et al. (2017) <DOI:10.1136/bmj.j573>) and model visualization.

Last updated 5 years ago

deft-approachmeta-analysissubgroup-analysis

6 stars 1.18 score 44 dependencies

IDConverter - Convert Identifiers in Biological Databases

Identifiers in biological databases connect different levels of metadata, phenotype data or genotype data. This tool is designed to easily convert identifiers within or between different biological databases (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557>).

Last updated 11 months ago

8 stars 1.08 score 20 dependencies

sigminer.prediction - Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures

Mutational signatures represent mutational processes occured in cancer evolution, thus are stable and genetic resources for subtyping. This tool provides functions for training neutral network models to predict the subtype a sample belongs to based on 'keras' and 'sigminer' packages.

Last updated 2 years ago

kerasmutational-signaturesprostate-cancersigminer

8 stars 0.91 score 136 dependencies

rsra - Query and Download SRA Files from NCBI

Query and download SRA files from NCBI with 'wget'.

Last updated 2 years ago

2 stars 0.23 score 25 dependencies

CNVMotif - Explore, Analyze and Visualize Catalogs and Patterns of Copy Number Variation in Cancer Genomics

Provides functionality for exploring, analyzing and visualizing the copy number variation (CNV) motifs in cancer genomics.

Last updated 2 years ago

sigminer

1 stars 0.09 score 128 dependencies

neopeptides - Calculate and Explore Property Indices of Neopeptides

Includes functions to calculate and explore several property indices for neopeptides, which are abnormal peptides generated from genome.

Last updated 3 years ago

immunotherapyneoantigenpeptides

1 stars 0.09 score 39 dependencies