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Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.

pypi: PACE
Data Quality of Experimental Data
Papers that mentioned: 13,779
Very Likely Science (90)
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
Very Likely Science (100)
cran: PRISMA
Protocol Inspection and State Machine Analysis
Papers that mentioned: 9,815
Very Likely Science (85)
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
Very Likely Science (100)
cran: lme4
Linear Mixed-Effects Models using 'Eigen' and S4
Papers that mentioned: 9,267
Very Likely Science (100)
pypi: PyMOL
Papers that mentioned: 8,266
Very Likely Science (90)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
cran: vegan
Community Ecology Package
Papers that mentioned: 6,903
Very Likely Science (100)
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
Very Likely Science (100)
cran: PERMANOVA
Multivariate Analysis of Variance Based on Distances and Permutations
Papers that mentioned: 6,292
Very Likely Science (85)
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
Very Likely Science (100)
pypi: TopHat
TopHat Platform
Papers that mentioned: 5,017
Very Likely Science (90)
cran: SAM
Sparse Additive Modelling
Papers that mentioned: 4,566
Very Likely Science (85)
cran: WGCNA
Weighted Correlation Network Analysis
Papers that mentioned: 3,479
Very Likely Science (85)
pypi: Facebook
Papers that mentioned: 3,274
Unlikely Science (0)
cran: nlme
Linear and Nonlinear Mixed Effects Models
Papers that mentioned: 3,265
Very Likely Science (100)
pypi: stats
Calculator-style statistical functions
Papers that mentioned: 3,105
Very Likely Science (90)
pypi: HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assays
Papers that mentioned: 3,071
Very Likely Science (65)
pypi: excel
This package name is reserved by Microsoft Corporation
Papers that mentioned: 2,995
Unlikely Science (5)
pypi: Zen
A simple way to access the ZenDesk v2 API via Python.
Papers that mentioned: 2,767
Very Likely Science (65)
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
Very Likely Science (75)
pypi: scikit-learn
A set of python modules for machine learning and data mining
Papers that mentioned: 2,431
Very Likely Science (100)
cran: MASS
Support Functions and Datasets for Venables and Ripley's MASS
Papers that mentioned: 2,353
Very Likely Science (100)
bioconductor: PAST
Pathway Association Study Tool (PAST)
Papers that mentioned: 2,336
Very Likely Science (100)
cran: PHENIX
Phenotypic Integration Index
Papers that mentioned: 2,287
Very Likely Science (75)
pypi: Circos
Circos plots in Python!
Papers that mentioned: 2,252
Very Likely Science (100)
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics data
Papers that mentioned: 2,223
Very Likely Science (75)
pypi: browser
A package to prevent Dependency Confusion attacks against Yandex.
Papers that mentioned: 2,125
Very Likely Science (65)
cran: gplots
Various R Programming Tools for Plotting Data
Papers that mentioned: 2,122
Very Likely Science (85)
pypi: analysis
Source code analysis of Python programs
Papers that mentioned: 2,036
Very Likely Science (90)
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
Very Likely Science (83)
pypi: Scaffold
Simple project scaffolding for Python
Papers that mentioned: 1,866
Very Likely Science (65)
cran: lmerTest
Tests in Linear Mixed Effects Models
Papers that mentioned: 1,865
Very Likely Science (100)
pypi: blast
a simple web-based, multi-platform music/mp3 player written in python, HTML/CSS and javascript
Papers that mentioned: 1,819
Very Likely Science (65)
cran: REST
RcmdrPlugin Easy Script Templates
Papers that mentioned: 1,757
Very Likely Science (75)
cran: pROC
Display and Analyze ROC Curves
Papers that mentioned: 1,740
Very Likely Science (95)
cran: Andromeda
Asynchronous Disk-Based Representation of Massive Data
Papers that mentioned: 1,724
Very Likely Science (85)
bioconductor: phyloseq
Handling and analysis of high-throughput microbiome census data
Papers that mentioned: 1,702
Very Likely Science (75)
cran: survival
Survival Analysis
Papers that mentioned: 1,690
Very Likely Science (100)
pypi: survival
Add static script_dir() method to Path
Papers that mentioned: 1,690
Very Likely Science (90)
cran: car
Companion to Applied Regression
Papers that mentioned: 1,651
Very Likely Science (100)
pypi: car
Papers that mentioned: 1,651
Unlikely Science (0)
cran: glmnet
Lasso and Elastic-Net Regularized Generalized Linear Models
Papers that mentioned: 1,607
Very Likely Science (100)
pypi: glmnet
Python wrapper for glmnet
Papers that mentioned: 1,607
Very Likely Science (100)
pypi: bowtie
Interactive Dashboard Toolkit.
Papers that mentioned: 1,566
Very Likely Science (90)
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
Very Likely Science (100)
cran: multcomp
Simultaneous Inference in General Parametric Models
Papers that mentioned: 1,558
Very Likely Science (75)
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555
Very Likely Science (100)
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
Very Likely Science (100)
cran: DA
Discriminant Analysis for Evolutionary Inference
Papers that mentioned: 1,541
Very Likely Science (95)
cran: Seurat
Tools for Single Cell Genomics
Papers that mentioned: 1,512
Very Likely Science (100)
pypi: CellProfiler
An open-source application for biological image analysis
Papers that mentioned: 1,504
Very Likely Science (100)
cran: survminer
Drawing Survival Curves using 'ggplot2'
Papers that mentioned: 1,473
Very Likely Science (75)
cran: randomForest
Breiman and Cutler's Random Forests for Classification and Regression
Papers that mentioned: 1,447
Very Likely Science (100)
pypi: custom
Custom self carry
Papers that mentioned: 1,363
Very Likely Science (65)
pypi: package
package is a package to package your package
Papers that mentioned: 1,300
Very Likely Science (65)
cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices
Papers that mentioned: 1,283
Very Likely Science (75)
cran: MuMIn
Multi-Model Inference
Papers that mentioned: 1,276
Very Likely Science (75)
pypi: 0
0
Papers that mentioned: 1,265
Very Likely Science (65)
cran: mgcv
Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Papers that mentioned: 1,251
Very Likely Science (75)
cran: RDP
The Ramer-Douglas-Peucker Algorithm
Papers that mentioned: 1,243
Very Likely Science (85)
cran: rms
Regression Modeling Strategies
Papers that mentioned: 1,236
Very Likely Science (100)
pypi: MACS
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,233
Very Likely Science (75)
pypi: for
Papers that mentioned: 1,226
Very Likely Science (65)
cran: dplyr
A Grammar of Data Manipulation
Papers that mentioned: 1,213
Very Likely Science (100)
cran: metafor
Meta-Analysis Package for R
Papers that mentioned: 1,205
Very Likely Science (100)
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203
Very Likely Science (100)
pypi: STAMP
A graphical software package for analyzing taxonomic and functional profiles.
Papers that mentioned: 1,190
Very Likely Science (65)
pypi: QuantStudio
Quant Studio
Papers that mentioned: 1,164
Very Likely Science (65)
cran: FactoMineR
Multivariate Exploratory Data Analysis and Data Mining
Papers that mentioned: 1,101
Very Likely Science (85)
cran: GA
Genetic Algorithms
Papers that mentioned: 1,091
Very Likely Science (100)
cran: psych
Procedures for Psychological, Psychometric, and Personality Research
Papers that mentioned: 1,085
Very Likely Science (100)
cran: corrplot
Visualization of a Correlation Matrix
Papers that mentioned: 1,077
Very Likely Science (100)
pypi: scipy
Fundamental algorithms for scientific computing in Python
Papers that mentioned: 1,071
Very Likely Science (100)
pypi: matplotlib
Python plotting package
Papers that mentioned: 1,045
Very Likely Science (100)
pypi: of
The Optimal Framework is the fastest path to building any modern multi-user system
Papers that mentioned: 1,025
Very Likely Science (65)
cran: tidyverse
Easily Install and Load the 'Tidyverse'
Papers that mentioned: 1,023
Very Likely Science (100)
cran: emmeans
Estimated Marginal Means, aka Least-Squares Means
Papers that mentioned: 1,009
Very Likely Science (100)
cran: OpenStreetMap
Access to Open Street Map Raster Images
Papers that mentioned: 1,001
Very Likely Science (100)
cran: Hmisc
Harrell Miscellaneous
Papers that mentioned: 1,000
Very Likely Science (75)
pypi: bwa
Bwa: Simple Notification Sender(Discord, Slack, Gmail and Telegram)
Papers that mentioned: 989
Very Likely Science (65)
bioconductor: affy
Methods for Affymetrix Oligonucleotide Arrays
Papers that mentioned: 989
Very Likely Science (98)
pypi: house
A lib to persist blobs by their sha256
Papers that mentioned: 960
Very Likely Science (65)
pypi: ape
A Productive Environment - make/rake/ant/fab-like system with support for FOSD
Papers that mentioned: 918
Very Likely Science (65)
cran: ape
Analyses of Phylogenetics and Evolution
Papers that mentioned: 918
Very Likely Science (100)
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
Papers that mentioned: 893
Very Likely Science (100)
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
Very Likely Science (100)
pypi: PICOS
A Python interface to conic optimization solvers.
Papers that mentioned: 859
Very Likely Science (100)
cran: ggpubr
'ggplot2' Based Publication Ready Plots
Papers that mentioned: 856
Very Likely Science (75)
bioconductor: MIRA
Methylation-Based Inference of Regulatory Activity
Papers that mentioned: 856
Very Likely Science (98)
pypi: fasta
The fasta python package enables you to deal with biological sequence files easily.
Papers that mentioned: 848
Very Likely Science (80)
cran: fasta
Fast Adaptive Shrinkage/Thresholding Algorithm
Papers that mentioned: 848
Very Likely Science (60)
pypi: numpy
Fundamental package for array computing in Python
Papers that mentioned: 832
Very Likely Science (100)
pypi: Pathway
Pathway is a data processing framework which takes care of streaming data updates for you.
Papers that mentioned: 827
Very Likely Science (75)
cran: lavaan
Latent Variable Analysis
Papers that mentioned: 814
Very Likely Science (100)
cran: ade4
Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Papers that mentioned: 809
Very Likely Science (85)
cran: Epi
Statistical Analysis in Epidemiology
Papers that mentioned: 805
Very Likely Science (85)
pypi: ggplot
ggplot for python
Papers that mentioned: 796
Very Likely Science (100)
cran: adegenet
Exploratory Analysis of Genetic and Genomic Data
Papers that mentioned: 767
Very Likely Science (100)
pypi: NEURON
Empirically-based simulator for modeling neurons and networks of neurons
Papers that mentioned: 766
Very Likely Science (100)