Packages with Software Mentions in Scientific Papers

bioconductor: frma

Frozen RMA and Barcode
Papers that mentioned: 26

Very Likely Science (90)

pypi: AHRS

Attitude and Heading Reference Systems.
Papers that mentioned: 26

Very Likely Science (65)

pypi: BitTorrent

UNKNOWN
Papers that mentioned: 26

Very Likely Science (65)

bioconductor: EBarrays

Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Papers that mentioned: 26

Very Likely Science (100)

pypi: n

Reserved name
Papers that mentioned: 26

Very Likely Science (65)

bioconductor: pcaExplorer

Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Papers that mentioned: 26

Very Likely Science (100)

pypi: BioGraph

Molecular graphs and the neural networks to embed them.
Papers that mentioned: 26

Very Likely Science (90)

pypi: Viper

Simple VTK based visualization software
Papers that mentioned: 26

Very Likely Science (90)

pypi: visualization

Visualization toolkit for the Berkeley AutoLab.
Papers that mentioned: 26

Very Likely Science (100)

pypi: homer

Configuration manager for network devices
Papers that mentioned: 26

Very Likely Science (90)

pypi: CLAM

Turns command-line tools into fully-fledged RESTful webservices with an auto-generated web-interface for human end-users.
Papers that mentioned: 26

Very Likely Science (100)

pypi: lib

Autocode standard library Python bindings
Papers that mentioned: 26

Very Likely Science (80)

bioconductor: QUBIC

An R package for qualitative biclustering in support of gene co-expression analyses
Papers that mentioned: 26

Very Likely Science (100)

pypi: sdm

Sparse Distributed Memory Framework
Papers that mentioned: 26

Very Likely Science (80)

pypi: skimage

Dummy package that points to scikit-image
Papers that mentioned: 26

Very Likely Science (100)

pypi: simpleM

My first Python package
Papers that mentioned: 26

Very Likely Science (65)

pypi: PEAS

Proximal Enrichment By Approximated Sampling
Papers that mentioned: 26

Very Likely Science (75)

pypi: Fold

A binary encoding scheme (optionally keyed)
Papers that mentioned: 26

Very Likely Science (65)

cran: shapes

Statistical Shape Analysis
Papers that mentioned: 26

Very Likely Science (93)

cran: DALY

The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R
Papers that mentioned: 26

Very Likely Science (75)

cran: Cyclops

Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
Papers that mentioned: 26

Very Likely Science (100)

pypi: seq2seq

Real valued sequence to sequence autoencoder
Papers that mentioned: 26

Very Likely Science (65)

cran: control

A Control Systems Toolbox
Papers that mentioned: 26

Very Likely Science (81)

pypi: d3heatmap

Python package to create interactive heatmap based on d3js.
Papers that mentioned: 26

Very Likely Science (80)

cran: CpGassoc

Association Between Methylation and a Phenotype of Interest
Papers that mentioned: 26

Very Likely Science (75)

bioconductor: PharmacoGx

Analysis of Large-Scale Pharmacogenomic Data
Papers that mentioned: 26

Very Likely Science (100)

cran: GMMAT

Generalized Linear Mixed Model Association Tests
Papers that mentioned: 26

Very Likely Science (83)

pypi: discovery

Python library for getting values from ETCD
Papers that mentioned: 26

Very Likely Science (65)

cran: LDcorSV

Linkage Disequilibrium Corrected by the Structure and the Relatedness
Papers that mentioned: 25

Very Likely Science (75)

cran: FMM

Rhythmic Patterns Modeling by FMM Models
Papers that mentioned: 25

Very Likely Science (100)

bioconductor: variancePartition

Quantify and interpret drivers of variation in multilevel gene expression experiments
Papers that mentioned: 25

Very Likely Science (100)

cran: perm

Exact or Asymptotic Permutation Tests
Papers that mentioned: 25

Very Likely Science (83)

cran: paran

Horn's Test of Principal Components/Factors
Papers that mentioned: 25

Very Likely Science (83)

pypi: Flight

This is building towards a flight simulation
Papers that mentioned: 25

Very Likely Science (75)

cran: MAMS

Designing Multi-Arm Multi-Stage Studies
Papers that mentioned: 25

Very Likely Science (75)

pypi: PEAK

The Python Enterprise Application Kit
Papers that mentioned: 25

Likely Science (40)

pypi: MolVS

Molecule Validation and Standardization
Papers that mentioned: 25

Very Likely Science (80)

pypi: PinPoint

A fast geo toolkit for academic affiliation strings
Papers that mentioned: 25

Very Likely Science (80)

bioconductor: conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Papers that mentioned: 25

Very Likely Science (100)

cran: TransPhylo

Inference of Transmission Tree from a Dated Phylogeny
Papers that mentioned: 25

Very Likely Science (75)

cran: migrate

Create Credit State Migration (Transition) Matrices
Papers that mentioned: 25

Very Likely Science (75)

cran: MasterBayes

ML and MCMC Methods for Pedigree Reconstruction and Analysis
Papers that mentioned: 25

Very Likely Science (93)

pypi: prime

Module with extremely simple functions based on prime numbers
Papers that mentioned: 25

Very Likely Science (65)

pypi: extraction

Extract basic info from HTML webpages.
Papers that mentioned: 25

Very Likely Science (65)

pypi: migrate

A simple language agnostic database migration tool
Papers that mentioned: 25

Very Likely Science (65)

cran: QRISK3

10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017)
Papers that mentioned: 25

Very Likely Science (75)

cran: diptest

Hartigan's Dip Test Statistic for Unimodality - Corrected
Papers that mentioned: 25

Very Likely Science (75)

pypi: perm

Papers that mentioned: 25

Very Likely Science (65)

bioconductor: PROPER

PROspective Power Evaluation for RNAseq
Papers that mentioned: 25

Very Likely Science (98)

cran: RaceID

Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Papers that mentioned: 25

Very Likely Science (75)

pypi: dadi

Fit population genetic models of demography and selection using diffusion approximations to the allele frequency spectrum
Papers that mentioned: 25

Very Likely Science (100)

bioconductor: CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Papers that mentioned: 25

Very Likely Science (100)

pypi: MetaPathways

MetaPathways is a modular pipeline to build PGDBs from Metagenomic sequences.
Papers that mentioned: 25

Very Likely Science (90)

cran: FI

Provide functions for forest inventory calculations
Papers that mentioned: 25

Very Likely Science (75)

cran: sqldf

Manipulate R Data Frames Using SQL
Papers that mentioned: 25

Very Likely Science (75)

pypi: sqldf

A simple way to run SQL queries (SQLite3) on pandas.Dataframe objects.
Papers that mentioned: 25

Very Likely Science (65)

pypi: CADET

CADET is a python interface to the CADET chromatography simulator
Papers that mentioned: 25

Very Likely Science (60)

pypi: MicrobeCensus

A command-line tool for estimating average genome size from shotgun sequence data
Papers that mentioned: 25

Very Likely Science (100)

pypi: plan

A Python package for writing and deploying cron jobs with a clear and beautiful syntax.
Papers that mentioned: 25

Very Likely Science (65)

pypi: PIMS

Python Image Sequence
Papers that mentioned: 25

Very Likely Science (100)

cran: seacarb

Seawater Carbonate Chemistry
Papers that mentioned: 25

Very Likely Science (85)

pypi: Assemble

Assemble: Assemble the packages!
Papers that mentioned: 25

Very Likely Science (65)

cran: DCGL

Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
Papers that mentioned: 25

Very Likely Science (85)

pypi: Mother

Mother is a Python Orm oriented to introspection and self autoadaption.
Papers that mentioned: 25

Very Likely Science (65)

pypi: DeepARG

Papers that mentioned: 25

Very Likely Science (65)

pypi: FMM

Numerical Computations
Papers that mentioned: 25

Very Likely Science (75)

cran: TSE

Total Survey Error
Papers that mentioned: 25

Very Likely Science (75)

cran: rvest

Easily Harvest (Scrape) Web Pages
Papers that mentioned: 25

Very Likely Science (83)

cran: httr

Tools for Working with URLs and HTTP
Papers that mentioned: 25

Very Likely Science (100)

bioconductor: cellHTS2

Analysis of cell-based screens - revised version of cellHTS
Papers that mentioned: 25

Very Likely Science (100)

pypi: cor

Distributed modular computing framework that runs anywhere
Papers that mentioned: 25

Very Likely Science (65)

pypi: dms

database management service dashboard
Papers that mentioned: 25

Very Likely Science (65)

pypi: SPE

Python IDE with Blender, Kiki, PyChecker, Remote debugger, Uml and wxGlade support
Papers that mentioned: 25

Very Likely Science (65)

pypi: velocyto

RNA velocity analysis for single cell RNA-seq data
Papers that mentioned: 25

Very Likely Science (90)

pypi: Rx

Reactive Extensions (Rx) for Python
Papers that mentioned: 25

Very Likely Science (65)

cran: HMP

Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP
Papers that mentioned: 25

Very Likely Science (75)

cran: SPECIES

Statistical Package for Species Richness Estimation
Papers that mentioned: 25

Very Likely Science (93)

cran: plan

Tools for Project Planning
Papers that mentioned: 25

Very Likely Science (95)

pypi: umap

UNIST synthesis MAP solution
Papers that mentioned: 24

Very Likely Science (65)

cran: TreeSim

Simulating Phylogenetic Trees
Papers that mentioned: 24

Very Likely Science (85)

bioconductor: MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics
Papers that mentioned: 24

Very Likely Science (100)

bioconductor: seqLogo

Sequence logos for DNA sequence alignments
Papers that mentioned: 24

Very Likely Science (100)

cran: SOP

Generalised Additive P-Spline Regression Models Estimation
Papers that mentioned: 24

Very Likely Science (85)

cran: fitTetra

fitTetra is an R package for assigning tetraploid genotype scores
Papers that mentioned: 24

Very Likely Science (75)

pypi: fit

FIT file I/O
Papers that mentioned: 24

Very Likely Science (65)

cran: LPmerge

Merging Linkage Maps by Linear Programming
Papers that mentioned: 24

Very Likely Science (83)

pypi: Comix

A GTK+ comic book viewer for .cbz, .cbr and .cbt files.
Papers that mentioned: 24

Very Likely Science (80)

cran: TMB

Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
Papers that mentioned: 24

Very Likely Science (100)

pypi: imblearn

Toolbox for imbalanced dataset in machine learning.
Papers that mentioned: 24

Very Likely Science (75)

pypi: ProtoNet

A lightweight, versatile framework for easy neural net prototyping and research
Papers that mentioned: 24

Very Likely Science (75)

pypi: sciplot

Format Matplotlib scientific plots
Papers that mentioned: 24

Very Likely Science (100)

cran: ipw

Estimate Inverse Probability Weights
Papers that mentioned: 24

Very Likely Science (80)

pypi: primer3plus

An easy-to-use Python API for Primer3 primer design.
Papers that mentioned: 24

Very Likely Science (100)

cran: EnvStats

Package for Environmental Statistics, Including US EPA Guidance
Papers that mentioned: 24

Very Likely Science (85)

pypi: kraken

OCR/HTR engine for all the languages
Papers that mentioned: 24

Very Likely Science (80)

cran: pcalg

Methods for Graphical Models and Causal Inference
Papers that mentioned: 24

Very Likely Science (75)

cran: Signac

Analysis of Single-Cell Chromatin Data
Papers that mentioned: 24

Very Likely Science (100)

cran: sciplot

Scientific Graphing Functions for Factorial Designs
Papers that mentioned: 24

Very Likely Science (93)

pypi: PRC

Python Remote Console
Papers that mentioned: 24

Very Likely Science (65)

cran: GRAPE

Gene-Ranking Analysis of Pathway Expression
Papers that mentioned: 24

Very Likely Science (93)