Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of GraphicsPapers that mentioned: 11,441
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distributionPapers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in RPapers that mentioned: 6,568
cran: PERMANOVA
Multivariate Analysis of Variance Based on Distances and PermutationsPapers that mentioned: 6,292
pypi: Facebook
Papers that mentioned: 3,274pypi: HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assaysPapers that mentioned: 3,071
pypi: scikit-learn
A set of python modules for machine learning and data miningPapers that mentioned: 2,431
cran: MASS
Support Functions and Datasets for Venables and Ripley's MASSPapers that mentioned: 2,353
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics dataPapers that mentioned: 2,223
pypi: browser
A package to prevent Dependency Confusion attacks against Yandex.Papers that mentioned: 2,125
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSetPapers that mentioned: 1,962
pypi: blast
a simple web-based, multi-platform music/mp3 player written in python, HTML/CSS and javascriptPapers that mentioned: 1,819
bioconductor: phyloseq
Handling and analysis of high-throughput microbiome census dataPapers that mentioned: 1,702
pypi: car
Papers that mentioned: 1,651cran: glmnet
Lasso and Elastic-Net Regularized Generalized Linear ModelsPapers that mentioned: 1,607
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing readsPapers that mentioned: 1,562
cran: randomForest
Breiman and Cutler's Random Forests for Classification and RegressionPapers that mentioned: 1,447
cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matricesPapers that mentioned: 1,283
cran: mgcv
Mixed GAM Computation Vehicle with Automatic Smoothness EstimationPapers that mentioned: 1,251
pypi: STAMP
A graphical software package for analyzing taxonomic and functional profiles.Papers that mentioned: 1,190
cran: FactoMineR
Multivariate Exploratory Data Analysis and Data MiningPapers that mentioned: 1,101
cran: psych
Procedures for Psychological, Psychometric, and Personality ResearchPapers that mentioned: 1,085
pypi: of
The Optimal Framework is the fastest path to building any modern multi-user systemPapers that mentioned: 1,025
pypi: bwa
Bwa: Simple Notification Sender(Discord, Slack, Gmail and Telegram)Papers that mentioned: 989
pypi: ape
A Productive Environment - make/rake/ant/fab-like system with support for FOSDPapers that mentioned: 918
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq dataPapers that mentioned: 893
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.Papers that mentioned: 893
pypi: fasta
The fasta python package enables you to deal with biological sequence files easily.Papers that mentioned: 848
pypi: Pathway
Pathway is a data processing framework which takes care of streaming data updates for you.Papers that mentioned: 827
cran: ade4
Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental SciencesPapers that mentioned: 809
pypi: NEURON
Empirically-based simulator for modeling neurons and networks of neuronsPapers that mentioned: 766