Showing 13 of total 13 results (show query)
jaredsmurray
bcf:Causal Inference for a Binary Treatment and Continuous Outcome using Bayesian Causal Forests
Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2020) <https://projecteuclid.org/journals/bayesian-analysis/volume-15/issue-3/Bayesian-Regression-Tree-Models-for-Causal-Inference--Regularization-Confounding/10.1214/19-BA1195.full> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.
Maintained by Jared S. Murray. Last updated 1 years ago.
69.1 match 41 stars 8.12 score 46 scripts
stochastictree
stochtree:Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference
Flexible stochastic tree ensemble software. Robust implementations of Bayesian Additive Regression Trees (BART) Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285> for supervised learning and Bayesian Causal Forests (BCF) Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195> for causal inference. Enables model serialization and parallel sampling and provides a low-level interface for custom stochastic forest samplers.
Maintained by Drew Herren. Last updated 18 days ago.
bartbayesian-machine-learningbayesian-methodsdecision-treesgradient-boosted-treesmachine-learningprobabilistic-modelstree-ensemblescpp
29.0 match 20 stars 8.52 score 40 scripts
bioc
Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.
dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp
9.1 match 28 stars 15.42 score 3.2k scripts 566 dependents
zhanxw
seqminer:Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Maintained by Xiaowei Zhan. Last updated 6 months ago.
annotationbcfbgenmeta-analysisnext-generation-sequencingplinksequencingtabixvcfworkflowzlibbzip2libzstdsqlite3cpp
16.3 match 30 stars 8.29 score 111 scripts 6 dependents
zilong-li
vcfppR:Rapid Manipulation of the Variant Call Format (VCF)
The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Maintained by Zilong Li. Last updated 3 days ago.
bioinformaticsfastrhtslibpopulation-geneticspopulation-genomicsvcfvcf-datavisulizationlibdeflatezlibbzip2xz-utilscurlcpp
8.9 match 13 stars 6.70 score 16 scripts
forestscientist
StemAnalysis:Reconstructing Tree Growth and Carbon Accumulation with Stem Analysis Data
Use stem analysis data to reconstructing tree growth and carbon accumulation. Users can independently or in combination perform a number of standard tasks for any tree species. (i) Age class determination. (ii) The cumulative growth, mean annual increment, and current annual increment of diameter at breast height (DBH) with bark, tree height, and stem volume with bark are estimated. (iii) Tree biomass and carbon storage estimation from volume and allometric models are calculated. (iv) Height-diameter relationship is fitted with nonlinear models, if diameter at breast height (DBH) or tree height are available, which can be used to retrieve tree height and diameter at breast height (DBH). <https://github.com/forestscientist/StemAnalysis>.
Maintained by Huili Wu. Last updated 2 years ago.
8.9 match 4 stars 4.38 score 12 scriptsbioc
SeqArray:Data Management of Large-Scale Whole-Genome Sequence Variant Calls
Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.
Maintained by Xiuwen Zheng. Last updated 10 days ago.
infrastructuredatarepresentationsequencinggeneticsbioinformaticsgds-formatsnpsnvweswgscpp
1.8 match 45 stars 12.08 score 1.1k scripts 9 dependentsbioc
AllelicImbalance:Investigates Allele Specific Expression
Provides a framework for allelic specific expression investigation using RNA-seq data.
Maintained by Jesper R Gadin. Last updated 5 months ago.
geneticsinfrastructuresequencing
3.1 match 5.08 score 7 scripts
yuanmingzhang
SEA:Segregation Analysis
A few major genes and a series of polygene are responsive for each quantitative trait. Major genes are individually identified while polygene is collectively detected. This is mixed major genes plus polygene inheritance analysis or segregation analysis (SEA). In the SEA, phenotypes from a single or multiple bi-parental segregation populations along with their parents are used to fit all the possible models and the best model of the trait for population phenotypic distributions is viewed as the model of the trait. There are fourteen types of population combinations available. Zhang Yuan-Ming, Gai Jun-Yi, Yang Yong-Hua (2003, <doi:10.1017/S0016672303006141>).
Maintained by Yuan-Ming Zhang. Last updated 3 years ago.
5.9 match 2.26 score 18 scripts
wheretrue
exonr:Scientific Data Processing
This package provides a set of tools for processing scientific data. It's based on the exon Rust package.
Maintained by Trent Hauck. Last updated 2 months ago.
arrowbioinformaticsdatafusionngsproteomicsrustsqlcargo
1.9 match 56 stars 5.27 score 2 scriptsbioc
alabaster.files:Wrappers to Save Common File Formats
Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.
Maintained by Aaron Lun. Last updated 5 months ago.
2.0 match 4.50 score 21 scripts
lbbe-software
rbioacc:Inference and Prediction of ToxicoKinetic (TK) Models
The MOSAICbioacc application is a turnkey package providing bioaccumulation factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances. See Ratier et al. (2021) <doi:10.1101/2021.09.08.459421>.
Maintained by Virgile Baudrot. Last updated 1 years ago.
0.5 match 4.78 score 8 scripts
