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annaffy - Annotation tools for Affymetrix biological metadata

Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.

Last updated

onechannelmicroarrayannotationgopathwaysreportwriting

5.70 score 3 dependents 69 scripts 772 downloads

fitnmr - Multidimensional Nuclear Magnetic Resonance Peak Fitting and Analysis

Tools for fitting and analyzing 1D-4D nuclear magnetic resonance spectra with analytical models of peak shapes and peak groups. The package reads spectra in 'NMRPipe' format, builds constrained parameter structures for chemical shifts, line widths, scalar couplings, volumes, and phases, and performs nonlinear least-squares optimization for iterative peak discovery or simultaneous fits across multiple spectra. It also provides methods for visualization, preprocessing, and kinetic analysis of 1D time-series data, including automated phase optimization, solvent suppression, time-domain correction for frequency shifts and line broadening, modeling spectra as linear combinations of two component spectra, and exponential rate fitting.

Last updated

5.38 score 2 stars 5 scripts 335 downloads

webbioc - Bioconductor Web Interface

An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)

Last updated

infrastructuremicroarrayonechanneldifferentialexpression

3.90 score 6 scripts 661 downloads

sparseLM - Interface to the 'sparseLM' Levenberg-Marquardt Library

Provides an R interface to the 'sparseLM' C library for large-scale nonlinear least squares problems with arbitrarily sparse Jacobians. The underlying solver implements a sparse variant of the Levenberg-Marquardt algorithm for minimizing sum-of-squares objective functions, supports user-supplied analytic Jacobians or finite-difference approximation, and is designed to exploit sparsity for improved memory use and performance. This package exposes the solver in R and uses sparse matrix classes and the 'CHOLMOD' sparse Cholesky factorization routines through the 'Matrix' package interface. Methods from the C library are described in Lourakis (2010) <doi:10.1007/978-3-642-15552-9_4>.

Last updated

3.30 score 300 downloads

deeppicker - R Interface to DEEP Picker for One- and Two-Dimensional Peak Picking

Provides an R interface to the DEEP Picker neural-network peak-picking tools for one- and two-dimensional NMR spectra. The package wraps the peak-picking engines, returning peak positions, intensities, line-shape parameters, and confidence scores. It also includes readers for supported spectrum formats, including NMRPipe, Sparky, TopSpin ASCII, JSON, CSV, and ldw files, so spectra can be imported and processed directly.

Last updated

cpp

1.70 score