Function-oriented Make-like declarative pipelines for statistics and data science are supported in the targets R package. As an extension to targets, the tarchetypes package provides convenient user-side functions to make targets easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the drake R package by Will Landau (2018) <doi:10.21105/joss.00550>.

cl-tar-file is a Common Lisp library that allows reading from and writing to various tar archive formats. Currently supported are the POSIX ustar, PAX (ustar with a few new entry types), GNU, and v7 (very old) formats.

This library is rather low level and is focused exclusively on reading and writing physical tar file entries using streams. Therefore, it contains no functionality for automatically building archives from a set of files on the filesystem or writing the contents of a file to the filesystem. Additionally, there are no smarts that read multiple physical entries and combine them into a single logical entry (e.g., with PAX extended headers or GNU long link/path name support). For a higher-level library that reads and writes logical entries, and also includes filesystem integration, see cl-tar.

This package provides a first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum is then assigned to the theoretical peptide with the best score, which is also referred to as the peptide to spectrum match (PSM). It is of course crucial for the downstream analysis to evaluate the quality of these matches. Therefore False Discovery Rate (FDR) control is used to return a reliable list PSMs. The FDR, however, requires a good characterisation of the score distribution of PSMs that are matched to the wrong peptide (bad target hits). In proteomics, the target decoy approach (TDA) is typically used for this purpose. The TDA method matches the spectra to a database of real (targets) and nonsense peptides (decoys). A popular approach to generate these decoys is to reverse the target database. Hence, all the PSMs that match to a decoy are known to be bad hits and the distribution of their scores are used to estimate the distribution of the bad scoring target PSMs. A crucial assumption of the TDA is that the decoy PSM hits have similar properties as bad target hits so that the decoy PSM scores are a good simulation of the target PSM scores. Users, however, typically do not evaluate these assumptions. To this end we developed TargetDecoy to generate diagnostic plots to evaluate the quality of the target decoy method.

This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.

This library provides a conduit-based, streaming interface for extracting and creating tar files.

tar-stream is a streaming tar parser and generator and nothing else. It is streams2 and operates purely using streams which means you can easily extract/parse tarballs without ever hitting the file system.

Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately).

Tarballs containing all the bootstrap binaries

Documentation at https://melpa.org/#/tardis-theme

Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak lists, and sample metadata required for a GC-MS analysis. The raw data has been restricted for demonstration purposes.

Software Heritage Tarball Loader

Creates tarballs for eggs in henrietta cache

Creates tarballs for eggs in henrietta cache

Documentation at https://melpa.org/#/ido-exit-target

An implementation of WHATWG EventTarget interface.

Binaries used to bootstrap the distribution.

This package provides a backport of CPython tarfile module.

Serve salmonella report files out of tar archives

This package defines basic interfaces to handle tar files. It is similar to fs.FS, but for tar files.

Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language of the GNU system. It is an implementation of the Scheme language which can be easily embedded in other applications to provide a convenient means of extending the functionality of the application without requiring the source code to be rewritten.

This package implements a functionality for pristinely disassembling a tar archive, and stashing needed raw bytes and offsets to reassemble a validating original archive.

GNU Binutils is a collection of tools for working with binary files. Perhaps the most notable are "ld", a linker, and "as", an assembler. Other tools include programs to display binary profiling information, list the strings in a binary file, and utilities for working with archives. The "bfd" library for working with executable and object formats is also included.

Headers of the Linux-Libre kernel.

Helper functions on Babel compilation targets