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idslme

IDSL.FSA:Fragmentation Spectra Analysis (FSA)

The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.

Maintained by Dinesh Barupal. Last updated 7 months ago.

fragmentation-spectramass-spectrometrymassbankmgfmgf-parsermspmsp-parserspectral-entropy

21.5 match 1 stars 3.48 score 2 dependents

bioc

MsBackendMgf:Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.

Maintained by RforMassSpectrometry Package Maintainer. Last updated 2 months ago.

infrastructureproteomicsmassspectrometrymetabolomicsdataimport

8.5 match 5 stars 7.32 score 35 scripts 4 dependents

epiforesite

facilityepimath:Analyze Mathematical Models of Healthcare Facility Transmission

Calculate useful quantities for a user-defined differential equation model of infectious disease transmission among individuals in a healthcare facility. Input rates of transition between states of individuals with and without the disease-causing organism, distributions of states at facility admission, relative infectivity of transmissible states, and the facility length of stay distribution. Calculate the model equilibrium and the basic facility reproduction number, as described in Toth et al. (2025) <doi:10.1101/2025.02.21.25322698>.

Maintained by Damon Toth. Last updated 5 days ago.

9.3 match 5.18 score

bioc

MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

Maintained by Laurent Gatto. Last updated 2 days ago.

immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp

3.6 match 130 stars 12.81 score 772 scripts 36 dependents

martinbladt

matrixdist:Statistics for Matrix Distributions

Tools for phase-type distributions including the following variants: continuous, discrete, multivariate, in-homogeneous, right-censored, and regression. Methods for functional evaluation, simulation and estimation using the expectation-maximization (EM) algorithm are provided for all models. The methods of this package are based on the following references. Asmussen, S., Nerman, O., & Olsson, M. (1996). Fitting phase-type distributions via the EM algorithm, Olsson, M. (1996). Estimation of phase-type distributions from censored data, Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60>, Albrecher, H., Bladt, M., & Yslas, J. (2022) <doi:10.1111/sjos.12505>, Albrecher, H., Bladt, M., Bladt, M., & Yslas, J. (2022) <doi:10.1016/j.insmatheco.2022.08.001>, Bladt, M., & Yslas, J. (2022) <doi:10.1080/03461238.2022.2097019>, Bladt, M. (2022) <doi:10.1017/asb.2021.40>, Bladt, M. (2023) <doi:10.1080/10920277.2023.2167833>, Albrecher, H., Bladt, M., & Mueller, A. (2023) <doi:10.1515/demo-2022-0153>, Bladt, M. & Yslas, J. (2023) <doi:10.1016/j.insmatheco.2023.02.008>.

Maintained by Martin Bladt. Last updated 17 days ago.

openblascppopenmp

10.5 match 1 stars 4.00 score 2 scripts

yufree

enviGCMS:GC/LC-MS Data Analysis for Environmental Science

Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.

Maintained by Miao YU. Last updated 2 months ago.

environmentmass-spectrometrymetabolomics

3.4 match 17 stars 6.49 score 30 scripts 1 dependents

robinhankin

hyper2:The Hyperdirichlet Distribution, Mark 2

A suite of routines for the hyperdirichlet distribution and reified Bradley-Terry; supersedes the 'hyperdirichlet' package; uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>. To cite in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>, and for Generalized Plackett-Luce likelihoods use Hankin 2024 <doi:10.18637/jss.v109.i08>.

Maintained by Robin K. S. Hankin. Last updated 3 days ago.

cpp

3.3 match 5 stars 6.01 score 38 scripts 1 dependents

taxonomicallyinformedannotation

tima:Taxonomically Informed Metabolite Annotation

This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.

Maintained by Adriano Rutz. Last updated 6 days ago.

metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome

2.0 match 9 stars 6.55 score 32 scripts 2 dependents

bioc

MsBackendMassbank:Mass Spectrometry Data Backend for MassBank record Files

Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.

Maintained by RforMassSpectrometry Package Maintainer. Last updated 18 days ago.

infrastructuremassspectrometrymetabolomicsdataimportmassbankspectra

1.8 match 3 stars 5.91 score 27 scripts

mcavs

doex:The One-Way Heteroscedastic ANOVA Tests

Contains the heteroscedastic ANOVA tests for normal and two-parameter exponential distributed populations. For normal distributions, Alexander-Govern test by Alexandern and Govern (1994) <doi:10.2307/1165140>, Alvandi et al. Generalized F test by Alvandi et al. (2012) <doi:10.1080/03610926.2011.573160>, Approximate F test by Asiribo and Gurland (1990) <doi:10.1080/03610929008830427>, Box F test by Box (1954) <doi:10.1214/aoms/1177728786>, Brown-Forsythe test by Brown and Forsythe (1974) <do:10.2307/1267501>, B2 test by Ozdemir and Kurt (2006) <http://sjam.selcuk.edu.tr/sjam/article/view/174>, Cochran F test by Cochran (1937) <https://www.jstor.org/stable/pdf/2984123.pdf>, Fiducial Approach test by Li et al. (2011) <doi:10.1016/j.csda.2010.12.009>, Generalized F test by Weerahandi (1995) <doi:10.2307/2532947>, Johansen F test by Johansen (1980) <doi:10.1093/biomet/67.1.85>, Modified Brown-Forsythe test by Mehrotra (1997) <doi:10.1080/03610919708813431>, Modified Welch test by Hartung et al.(2002) <doi:10.1007/s00362-002-0097-8>, One-Stage test by Chen and Chen (1998) <doi:10.1080/03610919808813501>, One-Stage Range test by Chen and Chen (2000) <doi:10.1080/01966324.2000.10737505>, Parametric Bootstrap test by Krishnamoorhty et al.(2007) <doi:10.1016/j.csda.2006.09.039>, Permutation F test by Berry and Mielke (2002) <doi:10.2466/pr0.2002.90.2.495>, Scott-Smith test by Scott and Smith (1971) <doi:10.2307/2346757>, Welch test by Welch(1951) <doi:10.2307/2332579>, and Welch-Aspin test by Aspin (1948) <doi:10.1093/biomet/35.1-2.88>. These tests are used to test the equality of group means under unequal variance. Also, a modified version of Generalized F-test is improved to test the equality of non-normal group means under unequal variances and a revised version of Generalized F-test is given to test the equality of non-normal group means caused by skewness. Furthermore, it consists some procedures for testing equality of several two-parameter exponentially distributed population means under unequal scale parameters such as generalized p-value, parametric bootstrap and fiducial approach test by Malekzadeh and Jafari (2019) <doi:10.1080/03610918.2018.1538452>. There is also Hsieh test by Hsieh (1986) <doi:10.2307/1270452> for testing equality of location parameters of two-parameter exponentially distributed populations under unequal scale parameters.

Maintained by Mustafa CAVUS. Last updated 5 years ago.

3.3 match 1.76 score 58 scripts

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