Packages with Software Mentions in Scientific Papers

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *in-vivo* transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.
Papers that mentioned: 1

Very Likely Science (85)

pypi: ingranalyze

Influence graph analysis, consistency check, diagnosis, repair and prediction.
Papers that mentioned: 1

Very Likely Science (90)

pypi: isi

sample test
Papers that mentioned: 1

Very Likely Science (65)

pypi: moment

Dealing with dates and times should be easy
Papers that mentioned: 1

Very Likely Science (65)

pypi: shmlast

An improved implementation of Conditional Reciprocal Best Hits with LAST and Python.
Papers that mentioned: 1

Very Likely Science (85)

pypi: inotify

An adapter to Linux kernel support for inotify directory-watching.
Papers that mentioned: 1

Very Likely Science (85)

cran: EFA.MRFA

Dimensionality Assessment Using Minimum Rank Factor Analysis
Papers that mentioned: 1

Very Likely Science (85)

cran: EcoNetGen

Simulate and Sample from Ecological Interaction Networks
Papers that mentioned: 1

Very Likely Science (100)

pypi: inmembrane

A bioinformatic pipeline for proteome annotation to predict if a protein is exposed on the surface of a bacteria.
Papers that mentioned: 1

Very Likely Science (100)

pypi: inner

a simple test
Papers that mentioned: 1

Very Likely Science (65)

pypi: Scavager

Proteomics post-search algorithm
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: attract

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Papers that mentioned: 1

Very Likely Science (100)

pypi: scattertext

An NLP package to visualize interesting terms in text.
Papers that mentioned: 1

Very Likely Science (81)

cran: ecolottery

Coalescent-Based Simulation of Ecological Communities
Papers that mentioned: 1

Very Likely Science (85)

pypi: moveit

ns_server master events analyzer
Papers that mentioned: 1

Very Likely Science (65)

pypi: instrumental

A condition/decision coverage tool for Python
Papers that mentioned: 1

Very Likely Science (65)

pypi: nocloud

Tools for creating a NoCloud image.
Papers that mentioned: 1

Very Likely Science (65)

pypi: pda

A command line todo list manager
Papers that mentioned: 1

Likely Science (40)

cran: easyalluvial

Generate Alluvial Plots with a Single Line of Code
Papers that mentioned: 1

Very Likely Science (75)

cran: stagePop

Modelling the Population Dynamics of a Stage-Structured Species in Continuous Time
Papers that mentioned: 1

Very Likely Science (93)

pypi: scatterbrain

Papers that mentioned: 1

Very Likely Science (65)

pypi: lmdb

Universal Python binding for the LMDB 'Lightning' Database
Papers that mentioned: 1

Very Likely Science (65)

cran: vhcub

Virus-Host Codon Usage Co-Adaptation Analysis
Papers that mentioned: 1

Very Likely Science (93)

cran: SPSL

Site Percolation on Square Lattices (SPSL)
Papers that mentioned: 1

Very Likely Science (75)

cran: chess

Read, Write, Create and Explore Chess Games
Papers that mentioned: 1

Likely Science (52)

cran: vhica

Vertical and Horizontal Inheritance Consistence Analysis
Papers that mentioned: 1

Very Likely Science (85)

pypi: ippai

Image Processing for Photoacoustic Imaging
Papers that mentioned: 1

Very Likely Science (65)

pypi: moltemplate

A general cross-platform text-based molecule builder for LAMMPS
Papers that mentioned: 1

Very Likely Science (100)

cran: checkpoint

Install Packages from Snapshots on the Checkpoint Server for Reproducibility
Papers that mentioned: 1

Very Likely Science (75)

cran: dupiR

Bayesian inference from count data using discrete uniform priors
Papers that mentioned: 1

Very Likely Science (85)

bioconductor: RefPlus

A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Papers that mentioned: 1

Very Likely Science (90)

pypi: serve

Pure python WSGI (PEP 333), CGI and web server classes
Papers that mentioned: 1

Very Likely Science (65)

cran: EbayesThresh

Empirical Bayes Thresholding and Related Methods
Papers that mentioned: 1

Very Likely Science (100)

cran: changer

Change R Package Name
Papers that mentioned: 1

Very Likely Science (95)

cran: DSWE

Data Science for Wind Energy
Papers that mentioned: 1

Very Likely Science (100)

pypi: morse

Convert strings to morse code.
Papers that mentioned: 1

Very Likely Science (65)

bioconductor: receptLoss

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
Papers that mentioned: 1

Very Likely Science (100)

pypi: intrepid

Fast Python
Papers that mentioned: 1

Very Likely Science (80)

cran: censys

Tools to Query the 'Censys' API
Papers that mentioned: 1

Very Likely Science (75)

pypi: systemd

systemd wrapper in Cython
Papers that mentioned: 1

Very Likely Science (65)

cran: SpNMF

Supervised NMF
Papers that mentioned: 1

Very Likely Science (75)

cran: splitTools

Tools for Data Splitting
Papers that mentioned: 1

Very Likely Science (75)

pypi: Moliere

Psycopg wrapper
Papers that mentioned: 1

Very Likely Science (65)

cran: splot

Simplified Plotting for Data Exploration
Papers that mentioned: 1

Very Likely Science (100)

cran: drtmle

Doubly-Robust Nonparametric Estimation and Inference
Papers that mentioned: 1

Very Likely Science (100)

pypi: intro

A simple hello world module
Papers that mentioned: 1

Very Likely Science (65)

cran: BayesGOF

Bayesian Modeling via Frequentist Goodness-of-Fit
Papers that mentioned: 1

Very Likely Science (93)

cran: ELISAtools

ELISA Data Analysis with Batch Correction
Papers that mentioned: 1

Very Likely Science (93)

pypi: services

A Python package for helpful tooling.
Papers that mentioned: 1

Very Likely Science (65)

pypi: intervaltree

Editable interval tree data structure for Python 2 and 3
Papers that mentioned: 1

Very Likely Science (100)

cran: spNNGP

Spatial Regression Models for Large Datasets using Nearest Neighbor Gaussian Processes
Papers that mentioned: 1

Very Likely Science (93)

cran: stminsights

A 'Shiny' Application for Inspecting Structural Topic Models
Papers that mentioned: 1

Very Likely Science (85)

bioconductor: antiProfiles

Implementation of gene expression anti-profiles
Papers that mentioned: 1

Very Likely Science (100)

cran: SPEDInstabR

Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept
Papers that mentioned: 1

Very Likely Science (75)

pypi: inter

Toolset for interactive command-line applications
Papers that mentioned: 1

Very Likely Science (65)

pypi: colour

converts and manipulates various color representation (HSL, RVB, web, X11, ...)
Papers that mentioned: 1

Very Likely Science (100)

pypi: ipopt

A Cython wrapper to the IPOPT optimization package
Papers that mentioned: 1

Very Likely Science (100)

pypi: ipp

Intel® Integrated Performance Primitives
Papers that mentioned: 1

Very Likely Science (80)

pypi: SBMLLint

Linter for SBML models.
Papers that mentioned: 1

Very Likely Science (100)

pypi: ipynb-py-convert

Convert .py files runnable in VSCode/Python or Atom/Hydrogen to jupyter .ipynb notebooks and vice versa
Papers that mentioned: 1

Very Likely Science (65)

pypi: neuroquery

Meta-analysis of neuroimaging studies.
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: RaggedExperiment

Representation of Sparse Experiments and Assays Across Samples
Papers that mentioned: 1

Very Likely Science (100)

cran: dotCall64

Enhanced Foreign Function Interface Supporting Long Vectors
Papers that mentioned: 1

Very Likely Science (75)

cran: DoTC

Distribution of Typicality Coefficients
Papers that mentioned: 1

Very Likely Science (75)

pypi: NeuroR

A morphology repair tool
Papers that mentioned: 1

Very Likely Science (100)

pypi: moiety-modeling

Moiety Modeling Implementation
Papers that mentioned: 1

Very Likely Science (100)

cran: spcr

Sparse Principal Component Regression
Papers that mentioned: 1

Very Likely Science (93)

cran: censusapi

Retrieve Data from the Census APIs
Papers that mentioned: 1

Very Likely Science (77)

pypi: industry

first dist
Papers that mentioned: 1

Very Likely Science (65)

pypi: impyute

Cross-sectional and time-series data imputation algorithms
Papers that mentioned: 1

Very Likely Science (90)

cran: xbreed

Genomic Simulation of Purebred and Crossbred Populations
Papers that mentioned: 1

Very Likely Science (85)

pypi: sho

Visualize python objects in the best way possible
Papers that mentioned: 1

Very Likely Science (65)

cran: ssc

Semi-Supervised Classification Methods
Papers that mentioned: 1

Very Likely Science (95)

pypi: isimage

A module and scripts for analysis of whole-mount in-situ hybridisation images.
Papers that mentioned: 1

Very Likely Science (95)

pypi: modus

A simple modeling python lib
Papers that mentioned: 1

Very Likely Science (65)

pypi: irt

Item Response Theory in Python
Papers that mentioned: 1

Very Likely Science (65)

bioconductor: qcmetrics

A Framework for Quality Control
Papers that mentioned: 1

Very Likely Science (100)

pypi: modular

Papers that mentioned: 1

Very Likely Science (65)

cran: distr6

The Complete R6 Probability Distributions Interface
Papers that mentioned: 1

Very Likely Science (100)

cran: stplanr

Sustainable Transport Planning
Papers that mentioned: 1

Very Likely Science (100)

cran: strand

A Framework for Investment Strategy Simulation
Papers that mentioned: 1

Very Likely Science (85)

cran: distcrete

Discrete Distribution Approximations
Papers that mentioned: 1

Very Likely Science (100)