Packages with Software Mentions in Scientific Papers

pypi: face

A command-line application framework (and CLI parser). Friendly for users, full-featured for developers.
Papers that mentioned: 6

Very Likely Science (65)

pypi: DomainFinder

Domain motion analysis for proteins
Papers that mentioned: 6

Very Likely Science (75)

cran: R2HTML

HTML Exportation for R Objects
Papers that mentioned: 6

Very Likely Science (95)

pypi: cif2cell

Construct a unit cell from CIF data
Papers that mentioned: 6

Very Likely Science (80)

pypi: dis

A simple test
Papers that mentioned: 6

Very Likely Science (65)

pypi: logger

Python logging helper
Papers that mentioned: 6

Very Likely Science (65)

cran: immunarch

Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Papers that mentioned: 6

Very Likely Science (100)

pypi: deepnet

package for deep learning
Papers that mentioned: 6

Very Likely Science (75)

pypi: fabia

Fabia Biclustering Algorithm
Papers that mentioned: 6

Very Likely Science (100)

cran: icenReg

Regression Models for Interval Censored Data
Papers that mentioned: 6

Very Likely Science (85)

pypi: Dandelion

A light weight deep learning framework
Papers that mentioned: 6

Very Likely Science (90)

cran: ScottKnott

The ScottKnott Clustering Algorithm
Papers that mentioned: 6

Very Likely Science (85)

pypi: faraway

Datasets and utilities to support books by Julian Faraway
Papers that mentioned: 6

Very Likely Science (65)

pypi: nbviewer

Jupyter Notebook Viewer
Papers that mentioned: 6

Very Likely Science (65)

pypi: detect

detect OS and Python versions
Papers that mentioned: 6

Very Likely Science (65)

cran: RSC

Robust and Sparse Correlation Matrix
Papers that mentioned: 6

Very Likely Science (85)

pypi: mxnet

Apache MXNet is an ultra-scalable deep learning framework. This version uses openblas and MKLDNN.
Papers that mentioned: 6

Very Likely Science (100)

cran: RVtests

Rare Variant Tests
Papers that mentioned: 6

Very Likely Science (75)

cran: RSE

Number of Newly Discovered Rare Species Estimation
Papers that mentioned: 6

Very Likely Science (75)

cran: natural

Estimating the Error Variance in a High-Dimensional Linear Model
Papers that mentioned: 6

Very Likely Science (93)

pypi: Wallace

An API for modeling data with psycopg2, redis-py, and pymongo.
Papers that mentioned: 6

Very Likely Science (75)

pypi: xyplot

Plotting with python made easy
Papers that mentioned: 6

Very Likely Science (75)

pypi: WhiteStripe

A wrapper for the WhiteStripe normalization R package
Papers that mentioned: 6

Very Likely Science (65)

pypi: visualize

useful visualization function
Papers that mentioned: 6

Very Likely Science (95)

pypi: Pythonic

Graphical automation tool
Papers that mentioned: 6

Very Likely Science (65)

pypi: WORC

Workflow for Optimal Radiomics Classification.
Papers that mentioned: 6

Very Likely Science (100)

pypi: spectral

Spectral Python (SPy) is a Python module for hyperspectral image processing.
Papers that mentioned: 6

Very Likely Science (80)

pypi: spreadsheet

A tool to manipulate Google Spreadsheets
Papers that mentioned: 6

Very Likely Science (65)

pypi: spot

DotCloud environment loader
Papers that mentioned: 6

Very Likely Science (65)

pypi: tablet

A tiny spreadsheet-like data structure and tool
Papers that mentioned: 6

Very Likely Science (65)

pypi: spyder

The Scientific Python Development Environment
Papers that mentioned: 6

Very Likely Science (90)

pypi: wallet

OpenAPI compliant library to access resources on the Wallet Inc. Platform
Papers that mentioned: 6

Likely Science (40)

pypi: synbio

Synbio design and build library
Papers that mentioned: 6

Very Likely Science (95)

pypi: webpack

Python bindings to Webpack
Papers that mentioned: 6

Very Likely Science (65)

pypi: walkway

Motion detector for a narrow runway
Papers that mentioned: 6

Very Likely Science (95)

pypi: VCF-kit

Assorted utilities for the variant call format
Papers that mentioned: 6

Very Likely Science (100)

pypi: pyserial

Python Serial Port Extension
Papers that mentioned: 6

Very Likely Science (65)

pypi: splatter

Vizualizing multidimensional points in a pleasing and informative way
Papers that mentioned: 6

Very Likely Science (65)

bioconductor: CHETAH

Fast and accurate scRNA-seq cell type identification
Papers that mentioned: 6

Very Likely Science (100)

cran: act

Aligned Corpus Toolkit
Papers that mentioned: 6

Very Likely Science (79)

pypi: MKS

A unit system based on meter, kilo, and second
Papers that mentioned: 6

Very Likely Science (65)

pypi: gram

gram: GitHub Repo Account Manager
Papers that mentioned: 6

Very Likely Science (65)

pypi: Saturn

Simple functions for tz-aware datetimes.
Papers that mentioned: 6

Very Likely Science (65)

pypi: gss

Tools for using GSS data in PyData.
Papers that mentioned: 6

Very Likely Science (65)

pypi: mlink

library for mlink
Papers that mentioned: 6

Very Likely Science (65)

cran: blavaan

Bayesian Latent Variable Analysis
Papers that mentioned: 6

Very Likely Science (93)

pypi: HeartBeat

Yet Another HeartBeat
Papers that mentioned: 6

Very Likely Science (65)

bioconductor: seqTools

Analysis of nucleotide, sequence and quality content on fastq files
Papers that mentioned: 6

Very Likely Science (100)

pypi: hit

Yet another command-line wrapper for Git.
Papers that mentioned: 6

Very Likely Science (65)

cran: canvasXpress

Visualization Package for CanvasXpress in R
Papers that mentioned: 6

Very Likely Science (74)

cran: cati

Community Assembly by Traits: Individuals and Beyond
Papers that mentioned: 6

Very Likely Science (99)

pypi: hts

Papers that mentioned: 6

Very Likely Science (65)

cran: coffee

Chronological Ordering for Fossils and Environmental Events
Papers that mentioned: 6

Very Likely Science (80)

cran: lidR

Airborne LiDAR Data Manipulation and Visualization for Forestry Applications
Papers that mentioned: 6

Very Likely Science (100)

cran: crrSC

Competing Risks Regression for Stratified and Clustered Data
Papers that mentioned: 6

Very Likely Science (85)

cran: deepnet

Deep Learning Toolkit in R
Papers that mentioned: 6

Very Likely Science (85)

pypi: modelr

Web Service like google charts API
Papers that mentioned: 6

Very Likely Science (95)

bioconductor: PrInCE

Predicting Interactomes from Co-Elution
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: qPLEXanalyzer

Tools for quantitative proteomics data analysis
Papers that mentioned: 6

Very Likely Science (100)

cran: SPAS

Stratified-Petersen Analysis System
Papers that mentioned: 6

Very Likely Science (85)

bioconductor: qrqc

Quick Read Quality Control
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: quantro

A test for when to use quantile normalization
Papers that mentioned: 6

Very Likely Science (98)

cran: doRNG

Generic Reproducible Parallel Backend for 'foreach' Loops
Papers that mentioned: 6

Very Likely Science (100)

pypi: mol

Top-level namespace for Autodesk Molecular tools.
Papers that mentioned: 6

Very Likely Science (75)

pypi: comp

Curses Omni Media Player
Papers that mentioned: 6

Likely Science (40)

cran: dtangle

Cell Type Deconvolution from Gene Expressions
Papers that mentioned: 6

Very Likely Science (93)

cran: geeM

Solve Generalized Estimating Equations
Papers that mentioned: 6

Very Likely Science (83)

pypi: Juno

A lightweight Python web framework
Papers that mentioned: 6

Very Likely Science (65)

pypi: panda

A Python implementation of the Panda REST interface
Papers that mentioned: 6

Very Likely Science (65)

cran: face

Fast Covariance Estimation for Sparse Functional Data
Papers that mentioned: 6

Very Likely Science (85)

bioconductor: cogena

co-expressed gene-set enrichment analysis
Papers that mentioned: 6

Very Likely Science (100)

pypi: morph

A collection of routines to help identify and morph objects.
Papers that mentioned: 6

Very Likely Science (65)

cran: abn

Modelling Multivariate Data with Additive Bayesian Networks
Papers that mentioned: 6

Very Likely Science (85)

cran: falcon

Finding Allele-Specific Copy Number in Next-Generation Sequencing Data
Papers that mentioned: 6

Very Likely Science (93)

bioconductor: countsimQC

Compare Characteristic Features of Count Data Sets
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: crlmm

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: cydar

Using Mass Cytometry for Differential Abundance Analyses
Papers that mentioned: 6

Very Likely Science (100)

cran: fastLink

Fast Probabilistic Record Linkage with Missing Data
Papers that mentioned: 6

Very Likely Science (100)

cran: fcros

A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations
Papers that mentioned: 6

Very Likely Science (60)

bioconductor: derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Papers that mentioned: 6

Very Likely Science (100)

pypi: magma

MAGnet MAnifest Management - Readout and create lists of magnets in yaml format.
Papers that mentioned: 6

Very Likely Science (65)

pypi: mouse

Hook and simulate mouse events on Windows and Linux
Papers that mentioned: 6

Very Likely Science (65)

cran: spatialreg

Spatial Regression Analysis
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: target

Predict Combined Function of Transcription Factors
Papers that mentioned: 6

Very Likely Science (100)

cran: gaston

Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Papers that mentioned: 6

Very Likely Science (85)

cran: LncPath

Identifying the Pathways Regulated by LncRNA Sets of Interest
Papers that mentioned: 6

Very Likely Science (85)

pypi: matplot

Papers that mentioned: 6

Very Likely Science (65)

cran: logger

A Lightweight, Modern and Flexible Logging Utility
Papers that mentioned: 6

Likely Science (50)

bioconductor: tradeSeq

trajectory-based differential expression analysis for sequencing data
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: drawProteins

Package to Draw Protein Schematics from Uniprot API output
Papers that mentioned: 6

Very Likely Science (100)

cran: ggrisk

Risk Score Plot for Cox Regression
Papers that mentioned: 6

Very Likely Science (85)

cran: Gifi

Multivariate Analysis with Optimal Scaling
Papers that mentioned: 6

Very Likely Science (93)

pypi: openstreetmap

OpenStreetMap coordinates
Papers that mentioned: 6

Very Likely Science (90)

cran: MDplot

Visualising Molecular Dynamics Analyses
Papers that mentioned: 6

Very Likely Science (100)

pypi: mrc

Read and write .mrc and .dv (deltavision) image file format
Papers that mentioned: 6

Very Likely Science (85)

pypi: mrcfile

MRC file I/O library
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: GOsummaries

Word cloud summaries of GO enrichment analysis
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: groHMM

GRO-seq Analysis Pipeline
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: GSAR

Gene Set Analysis in R
Papers that mentioned: 6

Very Likely Science (100)

bioconductor: GOfuncR

Gene ontology enrichment using FUNC
Papers that mentioned: 6

Very Likely Science (100)