Packages with Software Mentions in Scientific Papers

bioconductor: ATACseqQC

ATAC-seq Quality Control
Papers that mentioned: 14

Very Likely Science (100)

cran: snp.plotter

snp.plotter
Papers that mentioned: 14

Very Likely Science (75)

bioconductor: BAC

Papers that mentioned: 14

Unlikely Science (0)

cran: iml

Interpretable Machine Learning
Papers that mentioned: 14

Very Likely Science (96)

A wrapper around several APIs. Response is a request object, which is much extendable for custom error handling. The Available APIs are: EANData Locu Spoonacular Walmart Zomato
Papers that mentioned: 14

Very Likely Science (65)

pypi: nut

Network utility... things like a UDP/TCP relay.
Papers that mentioned: 14

Very Likely Science (65)

pypi: pdftotext

Simple PDF text extraction
Papers that mentioned: 14

Very Likely Science (65)

pypi: spike

Papers that mentioned: 14

Very Likely Science (65)

pypi: simba

Semantic similarity measures from Babylon Health
Papers that mentioned: 14

Very Likely Science (86)

cran: TIMP

Fitting Separable Nonlinear Models in Spectroscopy and Microscopy
Papers that mentioned: 14

Very Likely Science (76)

pypi: sra

A simple deploy tool
Papers that mentioned: 14

Very Likely Science (65)

pypi: puma

Python Unified Multi-tasking API (PUMA)
Papers that mentioned: 14

Very Likely Science (90)

pypi: POET

Calculate the orbital evolution of a planet-star system.
Papers that mentioned: 14

Very Likely Science (65)

pypi: sPyNNaker

Tools for simulating neural models generated using PyNN 0.9 on the SpiNNaker platform
Papers that mentioned: 14

Very Likely Science (100)

pypi: SpatialDE

Spatial and Temporal DE test
Papers that mentioned: 14

Very Likely Science (100)

pypi: PSCAD

A network toolkit that can be used to scan, sniff and discover hosts.
Papers that mentioned: 14

Very Likely Science (90)

pypi: pm

Command-line utility to manage development projects
Papers that mentioned: 14

Likely Science (40)

pypi: Taobao

Papers that mentioned: 14

Very Likely Science (65)

pypi: Velox

Batteries-included tooling for handling promotion, versioning, and zero-downtime requirments of Machine Learning models in production.
Papers that mentioned: 14

Very Likely Science (90)

pypi: uWSGI

The uWSGI server
Papers that mentioned: 14

Very Likely Science (65)

pypi: Markdown

Python implementation of John Gruber's Markdown.
Papers that mentioned: 14

Very Likely Science (100)

pypi: picardtools

python3 interface with Picard Tools from Broad institute
Papers that mentioned: 14

Very Likely Science (85)

pypi: Prestige

Pylot is a Flask extension that adds structure and map your views and templates together for rapid application development
Papers that mentioned: 14

Very Likely Science (65)

pypi: manta

A Python SDK for Joyent's Manta service
Papers that mentioned: 14

Very Likely Science (65)

cran: shinycssloaders

Add Loading Animations to a 'shiny' Output While It's Recalculating
Papers that mentioned: 14

Very Likely Science (75)

pypi: Party

Lightweight Python client to the Artifactory API.
Papers that mentioned: 14

Very Likely Science (65)

pypi: exp

Python tool do design and run experiments with global optimisation and grid search
Papers that mentioned: 14

Very Likely Science (95)

cran: flow

View and Browse Code Using Flow Diagrams
Papers that mentioned: 14

Very Likely Science (79)

pypi: glpk

PyGLPK, a Python module encapsulating GLPK.
Papers that mentioned: 14

Very Likely Science (80)

cran: precrec

Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves
Papers that mentioned: 14

Very Likely Science (100)

pypi: METER

Multi-state Estimates for Time-to-Event Research
Papers that mentioned: 14

Very Likely Science (75)

pypi: EukRep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
Papers that mentioned: 14

Very Likely Science (100)

cran: ggsn

North Symbols and Scale Bars for Maps Created with 'ggplot2' or 'ggmap'
Papers that mentioned: 14

Very Likely Science (75)

pypi: opencv-python

Wrapper package for OpenCV python bindings.
Papers that mentioned: 14

Very Likely Science (80)

bioconductor: RBM

RBM: a R package for microarray and RNA-Seq data analysis
Papers that mentioned: 14

Very Likely Science (100)

cran: polymapR

Linkage Analysis in Outcrossing Polyploids
Papers that mentioned: 14

Very Likely Science (85)

pypi: scikit-posthocs

Statistical post-hoc analysis and outlier detection algorithms
Papers that mentioned: 14

Very Likely Science (100)

cran: camtrapR

Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses
Papers that mentioned: 14

Very Likely Science (87)

cran: roxygen2

In-Line Documentation for R
Papers that mentioned: 14

Very Likely Science (100)

bioconductor: Repitools

Epigenomic tools
Papers that mentioned: 14

Very Likely Science (90)

pypi: molecular

A toolkit for molecular dynamics simulations
Papers that mentioned: 14

Very Likely Science (75)

pypi: Boris

Easily access and search Barclays bike availability in London, UK.
Papers that mentioned: 14

Very Likely Science (65)

cran: CTM

A Text Mining Toolkit for Chinese Document
Papers that mentioned: 14

Very Likely Science (75)

pypi: Florence

A Python based computational framework for integrated computer aided design, curvilinear mesh generation and finite and boundary element methods for linear and nonlinear analysis of solids and coupled multiphysics problems
Papers that mentioned: 14

Very Likely Science (75)

cran: DCluster

Functions for the Detection of Spatial Clusters of Diseases
Papers that mentioned: 14

Very Likely Science (75)

cran: DDD

Diversity-Dependent Diversification
Papers that mentioned: 14

Very Likely Science (75)

cran: LLM

Logit Leaf Model Classifier for Binary Classification
Papers that mentioned: 14

Very Likely Science (75)

cran: motif

Local Pattern Analysis
Papers that mentioned: 14

Very Likely Science (85)

pypi: flow

columnflow
Papers that mentioned: 14

Likely Science (55)

cran: yaml

Methods to Convert R Data to YAML and Back
Papers that mentioned: 14

Very Likely Science (100)

cran: matR

Metagenomics Analysis Tools
Papers that mentioned: 14

Very Likely Science (85)

pypi: me

me
Papers that mentioned: 14

Very Likely Science (65)

cran: mri

Modified Rand and Wallace Indices
Papers that mentioned: 14

Very Likely Science (83)

cran: LOST

Missing Morphometric Data Simulation and Estimation
Papers that mentioned: 14

Very Likely Science (93)

bioconductor: trackViewer

A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Papers that mentioned: 14

Very Likely Science (100)

cran: unmarked

Models for Data from Unmarked Animals
Papers that mentioned: 14

Very Likely Science (100)

pypi: EB

Ensemble Builder
Papers that mentioned: 14

Very Likely Science (65)

pypi: microsoft

This package name is reserved by Microsoft Corporation
Papers that mentioned: 14

Unlikely Science (5)

pypi: mri

Papers that mentioned: 14

Unlikely Science (0)

bioconductor: cqn

Conditional quantile normalization
Papers that mentioned: 14

Very Likely Science (90)

pypi: neo4j

Neo4j Bolt driver for Python
Papers that mentioned: 14

Very Likely Science (65)

pypi: entropy

entropy is a command line friend that helps you reduce entropy in your life
Papers that mentioned: 14

Very Likely Science (65)

bioconductor: SGSeq

Splice event prediction and quantification from RNA-seq data
Papers that mentioned: 14

Very Likely Science (75)

pypi: AIDE

AguaClara Infrastructure Design Engine
Papers that mentioned: 14

Very Likely Science (100)

pypi: umap-learn

Uniform Manifold Approximation and Projection
Papers that mentioned: 13

Very Likely Science (100)

cran: sirt

Supplementary Item Response Theory Models
Papers that mentioned: 13

Very Likely Science (83)

pypi: v

v makes building projects easier. It's as simple as that.
Papers that mentioned: 13

Very Likely Science (65)

pypi: pingouin

Pingouin: statistical package for Python
Papers that mentioned: 13

Very Likely Science (90)

cran: TTR

Technical Trading Rules
Papers that mentioned: 13

Very Likely Science (75)

cran: IFP

Identifying Functional Polymorphisms
Papers that mentioned: 13

Very Likely Science (83)

cran: kml

K-Means for Longitudinal Data
Papers that mentioned: 13

Very Likely Science (75)

pypi: metaMS

Data processing, and annotation for metabolomics analysis by low-resolution GC-MS
Papers that mentioned: 13

Very Likely Science (75)

cran: apaTables

Create American Psychological Association (APA) Style Tables
Papers that mentioned: 13

Very Likely Science (99)

pypi: c3d

A library for manipulating C3D binary files
Papers that mentioned: 13

Very Likely Science (100)

bioconductor: PathNet

An R package for pathway analysis using topological information
Papers that mentioned: 13

Very Likely Science (100)

bioconductor: Mergeomics

Integrative network analysis of omics data
Papers that mentioned: 13

Very Likely Science (85)

cran: BSL

Bayesian Synthetic Likelihood
Papers that mentioned: 13

Very Likely Science (93)

cran: MAPA

Multiple Aggregation Prediction Algorithm
Papers that mentioned: 13

Very Likely Science (85)

cran: JMI

Jackknife Mutual Information
Papers that mentioned: 13

Very Likely Science (83)

bioconductor: singscore

Rank-based single-sample gene set scoring method
Papers that mentioned: 13

Very Likely Science (100)

cran: DTComPair

Comparison of Binary Diagnostic Tests in a Paired Study Design
Papers that mentioned: 13

Very Likely Science (75)

pypi: Orpheus

An intelligent music retrieval engine
Papers that mentioned: 13

Likely Science (40)

pypi: spline

(s)hell oriented (p)ipe(line) tool for ci/cd
Papers that mentioned: 13

Very Likely Science (65)

pypi: QIP

Quantum Computing Library
Papers that mentioned: 13

Very Likely Science (65)

pypi: smart

Smart Package Manager is a next generation package handling tool
Papers that mentioned: 13

Very Likely Science (65)

pypi: UPnP

Forward a Port with UPnP and pure Python script
Papers that mentioned: 13

Very Likely Science (65)

pypi: simulate

HuggingFace community-driven open-source library of simulation environments
Papers that mentioned: 13

Very Likely Science (100)

pypi: popgen

Synthetic Population Generator 2.0
Papers that mentioned: 13

Very Likely Science (65)

pypi: pcap

packet capture library
Papers that mentioned: 13

Very Likely Science (65)

pypi: trackpy

particle-tracking toolkit
Papers that mentioned: 13

Very Likely Science (100)

pypi: SLIP

SLIP: a Simple Library for Image Processing
Papers that mentioned: 13

Very Likely Science (100)

pypi: StochPy

StochPy (Stochastic modeling in Python) provides several stochastic simulation algorithms to simulate (bio)chemical systems of reactions in a stochastic manner.
Papers that mentioned: 13

Very Likely Science (90)