Packages with Software Mentions in Scientific Papers

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Papers that mentioned: 14

Very Likely Science (100)

cran: predictmeans

Predicted Means for Linear and Semiparametric Models
Papers that mentioned: 14

Very Likely Science (80)

pypi: pm

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

Likely Science (40)

pypi: local

To browse local files.
Papers that mentioned: 14

Very Likely Science (65)

pypi: NanoSV

Structural variation detection tool for Oxford Nanopore data.
Papers that mentioned: 14

Very Likely Science (100)

cran: SDAR

Stratigraphic Data Analysis
Papers that mentioned: 14

Very Likely Science (93)

pypi: deal

**Deal** is a Python library for [design by contract][wiki] (DbC) programming.
Papers that mentioned: 14

Very Likely Science (100)

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)

cran: sra

Selection Response Analysis
Papers that mentioned: 14

Very Likely Science (85)

pypi: gseapy

Gene Set Enrichment Analysis in Python
Papers that mentioned: 14

Very Likely Science (100)

pypi: puma

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

Very Likely Science (90)

pypi: Markdown

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

Very Likely Science (100)

cran: deal

Learning Bayesian Networks with Mixed Variables
Papers that mentioned: 14

Very Likely Science (85)

pypi: EINSTEIN

Useful speech recognition and transcription related library for Indian languages.
Papers that mentioned: 14

Very Likely Science (65)

pypi: uWSGI

The uWSGI server
Papers that mentioned: 14

Very Likely Science (65)

bioconductor: DropletUtils

Utilities for Handling Single-Cell Droplet Data
Papers that mentioned: 14

Very Likely Science (90)

cran: GiRaF

Gibbs Random Fields Analysis
Papers that mentioned: 14

Very Likely Science (85)

cran: pcnetmeta

Patient-Centered Network Meta-Analysis
Papers that mentioned: 14

Very Likely Science (93)

cran: R.matlab

Read and Write MAT Files and Call MATLAB from Within R
Papers that mentioned: 14

Very Likely Science (75)

pypi: sra

A simple deploy tool
Papers that mentioned: 14

Very Likely Science (65)

cran: precrec

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

Very Likely Science (100)

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)

cran: POET

Principal Orthogonal ComplEment Thresholding (POET) Method
Papers that mentioned: 14

Likely Science (50)

pypi: EukRep

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

Very Likely Science (100)

pypi: POET

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

Very Likely Science (65)

pypi: dammit

dammit!
Papers that mentioned: 14

Very Likely Science (100)

bioconductor: GlobalAncova

Global test for groups of variables via model comparisons
Papers that mentioned: 14

Very Likely Science (90)

cran: LIM

Linear Inverse Model Examples and Solution Methods
Papers that mentioned: 14

Very Likely Science (75)

pypi: TEtranscripts

Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
Papers that mentioned: 14

Very Likely Science (90)

pypi: gs

A minimalistic Google Storage client
Papers that mentioned: 14

Very Likely Science (65)

pypi: SCSA

A novel algorithm for signal representation and denoising
Papers that mentioned: 14

Very Likely Science (75)

pypi: PSCAD

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

Very Likely Science (90)

pypi: SpatialDE

Spatial and Temporal DE test
Papers that mentioned: 14

Very Likely Science (100)

cran: vars

VAR Modelling
Papers that mentioned: 14

Very Likely Science (85)

pypi: nut

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

Very Likely Science (65)

pypi: flow

columnflow
Papers that mentioned: 14

Likely Science (55)

cran: CTM

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

Very Likely Science (75)

pypi: pylab

Papers that mentioned: 14

Unlikely Science (0)

pypi: reg

Clever dispatch
Papers that mentioned: 14

Very Likely Science (65)

bioconductor: cqn

Conditional quantile normalization
Papers that mentioned: 14

Very Likely Science (90)

cran: argosfilter

Argos Locations Filter
Papers that mentioned: 14

Very Likely Science (75)

pypi: me

me
Papers that mentioned: 14

Very Likely Science (65)

pypi: evaluation

A tool for compare the difference of the files.
Papers that mentioned: 14

Very Likely Science (65)

cran: ANN2

Artificial Neural Networks for Anomaly Detection
Papers that mentioned: 14

Very Likely Science (95)

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)

pypi: EB

Ensemble Builder
Papers that mentioned: 14

Very Likely Science (65)

cran: rfishbase

R Interface to 'FishBase'
Papers that mentioned: 14

Very Likely Science (100)

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)

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: roxygen2

In-Line Documentation for R
Papers that mentioned: 14

Very Likely Science (100)

pypi: MDP

MDP is a Python library for building complex data processing software by combining widely used machine learning algorithms into pipelines and networks.
Papers that mentioned: 14

Very Likely Science (90)

cran: mri

Modified Rand and Wallace Indices
Papers that mentioned: 14

Very Likely Science (83)

cran: ETAS

Modeling Earthquake Data Using 'ETAS' Model
Papers that mentioned: 14

Very Likely Science (100)

cran: LLM

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

Very Likely Science (75)

cran: MAPA

Multiple Aggregation Prediction Algorithm
Papers that mentioned: 13

Very Likely Science (85)

cran: DTComPair

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

Very Likely Science (75)

pypi: CDR

这是第一个对外发布的模块
Papers that mentioned: 13

Very Likely Science (65)

pypi: v

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

Very Likely Science (65)

cran: BSL

Bayesian Synthetic Likelihood
Papers that mentioned: 13

Very Likely Science (93)

cran: JMI

Jackknife Mutual Information
Papers that mentioned: 13

Very Likely Science (83)

bioconductor: Mergeomics

Integrative network analysis of omics data
Papers that mentioned: 13

Very Likely Science (85)

cran: RGCCA

Regularized and Sparse Generalized Canonical Correlation Analysis for Multiblock Data
Papers that mentioned: 13

Very Likely Science (85)

pypi: pingouin

Pingouin: statistical package for Python
Papers that mentioned: 13

Very Likely Science (90)

cran: kml

K-Means for Longitudinal Data
Papers that mentioned: 13

Very Likely Science (75)

pypi: mimics

Small tool for deferring actions and operations on objects and classes
Papers that mentioned: 13

Very Likely Science (65)

cran: eggCounts

Hierarchical Modelling of Faecal Egg Counts
Papers that mentioned: 13

Very Likely Science (85)

pypi: Zope

Zope application server / web framework
Papers that mentioned: 13

Very Likely Science (65)

pypi: short

A simple short implementation for Python3
Papers that mentioned: 13

Very Likely Science (65)

bioconductor: Chicago

CHiCAGO: Capture Hi-C Analysis of Genomic Organization
Papers that mentioned: 13

Very Likely Science (100)

cran: yarrr

A Companion to the e-Book "YaRrr!: The Pirate's Guide to R"
Papers that mentioned: 13

Very Likely Science (75)

pypi: pcap

packet capture library
Papers that mentioned: 13

Very Likely Science (65)

pypi: Hawk

Easy setup tool for Rackspace Cloud Monitoring
Papers that mentioned: 13

Very Likely Science (65)

cran: clusterRepro

Reproducibility of Gene Expression Clusters
Papers that mentioned: 13

Very Likely Science (93)

pypi: graphmap

Images on a quad graph. Create an infinite canvas
Papers that mentioned: 13

Very Likely Science (65)

pypi: cron

cron
Papers that mentioned: 13

Very Likely Science (65)

cran: smacof

Multidimensional Scaling
Papers that mentioned: 13

Very Likely Science (83)

pypi: UPnP

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

Very Likely Science (65)

cran: FREQ

Estimate population size from capture frequencies
Papers that mentioned: 13

Very Likely Science (75)

bioconductor: ggcyto

Visualize Cytometry data with ggplot
Papers that mentioned: 13

Very Likely Science (100)

pypi: leaflet

Dead simple I2P SAM library
Papers that mentioned: 13

Very Likely Science (90)

cran: AGD

Analysis of Growth Data
Papers that mentioned: 13

Very Likely Science (87)

cran: sjmisc

Data and Variable Transformation Functions
Papers that mentioned: 13

Very Likely Science (100)

pypi: ESN

Multiple Layer ESN
Papers that mentioned: 13

Very Likely Science (65)

cran: pRF

Permutation Significance for Random Forests
Papers that mentioned: 13

Very Likely Science (83)

bioconductor: GARS

GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets
Papers that mentioned: 13

Very Likely Science (85)

pypi: ImmuneDB

A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
Papers that mentioned: 13

Very Likely Science (100)

cran: omics

'–omics' Data Analysis Toolbox
Papers that mentioned: 13

Very Likely Science (85)

cran: comparison

Multivariate Likelihood Ratio Calculation and Evaluation
Papers that mentioned: 13

Very Likely Science (88)

pypi: DBN

Decentralized Bluetooth Network
Papers that mentioned: 13

Very Likely Science (75)

pypi: ipad

A silly util package
Papers that mentioned: 13

Very Likely Science (65)