Showing 8 of total 8 results (show query)
bioc
CODEX:A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.
Maintained by Yuchao Jiang. Last updated 5 months ago.
immunooncologyexomeseqnormalizationqualitycontrolcopynumbervariation
59.7 match 5.30 score 33 scripts 1 dependents
mmi-codex
Xcertainty:Estimating Lengths and Uncertainty from Photogrammetric Imagery
Implementation of Bayesian models for estimating object lengths and morphological relationships between object lengths using photographic data collected from drones. The Bayesian model is described in "Bayesian approach for predicting photogrammetric uncertainty in morphometric measurements derived from drones" (Bierlich et al., 2021, <doi:10.3354/meps13814>).
Maintained by K.C. Bierlich. Last updated 5 months ago.
15.0 match 3 stars 5.91 score 10 scripts
igordot
phenomenalist:Analysis Toolkit for PhenoCycler (CODEX) Data in R
A collection of tools for cleaning, clustering, and plotting PhenoCycler (CODEX) data.
Maintained by Igor Dolgalev. Last updated 1 years ago.
14.5 match 3 stars 2.18 score 1 scripts
satijalab
Seurat:Tools for Single Cell Genomics
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Maintained by Paul Hoffman. Last updated 1 years ago.
human-cell-atlassingle-cell-genomicssingle-cell-rna-seqcpp
1.8 match 2.4k stars 16.86 score 50k scripts 73 dependentsbioc
iCNV:Integrated Copy Number Variation detection
Integrative copy number variation (CNV) detection from multiple platform and experimental design.
Maintained by Zilu Zhou. Last updated 5 months ago.
immunooncologyexomeseqwholegenomesnpcopynumbervariationhiddenmarkovmodel
5.1 match 4.30 score 5 scriptsbioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 16 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
2.3 match 22 stars 8.59 score 69 scripts
aminadibi
codexcopd:The CODEX (Comorbidity, Obstruction, Dyspnea, and Previous Severe Exacerbations) Index: Short and Medium-Term Prognosis in Patients Hospitalized for Chronic Obstructive Pulmonary Disease (COPD) Exacerbations
Predicts 3 to 12 months prognosis in Chronic Obstructive Pulmonary Disease (COPD) patients hospitalized for severe exacerbations, as described in Almagro et al. (2014) <doi:10.1378/chest.13-1328>.
Maintained by Amin Adibi. Last updated 5 years ago.
7.6 match 1.70 score
lionelvoirol
idarps:Datasets and Functions for the Class "Modelling and Data Analysis for Pharmaceutical Sciences"
Provides datasets and functions for the class "Modelling and Data Analysis for Pharmaceutical Sciences". The datasets can be used to present various methods of data analysis and statistical modeling. Functions for data visualization are also implemented.
Maintained by Lionel Voirol. Last updated 11 months ago.
6.6 match 1.70 score 6 scripts