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.

bioconductor: ballgown
Flexible, isoform-level differential expression analysis
Papers that mentioned: 21
cran: robustlmm
Robust Linear Mixed Effects Models
Papers that mentioned: 21
pypi: build
A simple, correct Python build frontend
Papers that mentioned: 21
cran: kableExtra
Construct Complex Table with 'kable' and Pipe Syntax
Papers that mentioned: 21
cran: curl
A Modern and Flexible Web Client for R
Papers that mentioned: 21
pypi: display
simple printer of nested list
Papers that mentioned: 21
pypi: PyVCF
Variant Call Format (VCF) parser for Python
Papers that mentioned: 21
bioconductor: DTA
Dynamic Transcriptome Analysis
Papers that mentioned: 21
cran: optimx
Expanded Replacement and Extension of the 'optim' Function
Papers that mentioned: 21
cran: OpenML
Open Machine Learning and Open Data Platform
Papers that mentioned: 21
pypi: Moose
Your manager for endless iterative tasks.
Papers that mentioned: 21
pypi: frappe
Frappe placeholder package
Papers that mentioned: 21
pypi: biotools
A bunch of bioinformatics utilities.
Papers that mentioned: 21
cran: bayestestR
Understand and Describe Bayesian Models and Posterior Distributions
Papers that mentioned: 21
cran: MF
Mitigated Fraction
Papers that mentioned: 21
pypi: pip
The PyPA recommended tool for installing Python packages.
Papers that mentioned: 21
pypi: snow
Python asyncio library for ServiceNow
Papers that mentioned: 21
cran: ClustOfVar
Clustering of Variables
Papers that mentioned: 21
cran: nloptr
R Interface to NLopt
Papers that mentioned: 21
cran: RPS
Resistant Procrustes Superimposition
Papers that mentioned: 21
cran: DET
Papers that mentioned: 21
pypi: XAS

Papers that mentioned: 21
pypi: pyplot
Python plotting package
Papers that mentioned: 21
pypi: research
Utility modules used for research and/or learning
Papers that mentioned: 21
cran: paleotree
Paleontological and Phylogenetic Analyses of Evolution
Papers that mentioned: 21
pypi: librosa
Python module for audio and music processing
Papers that mentioned: 21
pypi: bcbio
UNKNOWN
Papers that mentioned: 20
cran: boa
Bayesian Output Analysis Program (BOA) for MCMC
Papers that mentioned: 20
cran: blmeco
Data Files and Functions Accompanying the Book "Bayesian Data Analysis in Ecology using R, BUGS and Stan"
Papers that mentioned: 20
bioconductor: MEDME
Modelling Experimental Data from MeDIP Enrichment
Papers that mentioned: 20
cran: itsadug
Interpreting Time Series and Autocorrelated Data Using GAMMs
Papers that mentioned: 20
cran: PropCIs
Various Confidence Interval Methods for Proportions
Papers that mentioned: 20
cran: cvAUC
Cross-Validated Area Under the ROC Curve Confidence Intervals
Papers that mentioned: 20
pypi: quadprog
Quadratic Programming Solver
Papers that mentioned: 20
bioconductor: maanova
Tools for analyzing Micro Array experiments
Papers that mentioned: 20
pypi: Manifold
An SMF service manifest creation tool.
Papers that mentioned: 20
bioconductor: SRAdb
A compilation of metadata from NCBI SRA and tools
Papers that mentioned: 20
cran: rsm
Response-Surface Analysis
Papers that mentioned: 20
cran: mapplots
Data Visualisation on Maps
Papers that mentioned: 20
cran: apcluster
Affinity Propagation Clustering
Papers that mentioned: 20
cran: SAMM
Some Algorithms for Mixed Models
Papers that mentioned: 20
pypi: Lasagne
A lightweight library to build and train neural networks in Theano
Papers that mentioned: 20
pypi: dryad
A pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.
Papers that mentioned: 20
cran: ADMM
Algorithms using Alternating Direction Method of Multipliers
Papers that mentioned: 20
pypi: argparse
Python command-line parsing library
Papers that mentioned: 20
pypi: solver
Math problem solver
Papers that mentioned: 20
cran: EMP
Expected Maximum Profit Classification Performance Measure
Papers that mentioned: 20
pypi: Hummingbird
An API Wrapper for Hummingbird.me
Papers that mentioned: 20
cran: Rfit
Rank-Based Estimation for Linear Models
Papers that mentioned: 20
pypi: POT
Python Optimal Transport Library
Papers that mentioned: 20
pypi: Zorro
Network communication library, with zeromq support
Papers that mentioned: 20
cran: RHRV
Heart Rate Variability Analysis of ECG Data
Papers that mentioned: 20
cran: Rmpi
Interface (Wrapper) to MPI (Message-Passing Interface)
Papers that mentioned: 20
cran: GSE
Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data
Papers that mentioned: 20
bioconductor: POMA
Tools for Omics Data Analysis
Papers that mentioned: 20
bioconductor: PCAtools
PCAtools: Everything Principal Components Analysis
Papers that mentioned: 20
cran: EGRET
Exploration and Graphics for RivEr Trends
Papers that mentioned: 20
cran: relsurv
Relative Survival
Papers that mentioned: 20
pypi: skyline
Papers that mentioned: 20
bioconductor: ROTS
Reproducibility-Optimized Test Statistic
Papers that mentioned: 20
pypi: gls
Gaussian Likelihood scoring method.
Papers that mentioned: 20
pypi: pyGenomeTracks
Command-line tool to make beautiful and reproducible genome browser snapshots
Papers that mentioned: 20
cran: POT
Generalized Pareto Distribution and Peaks Over Threshold
Papers that mentioned: 20
pypi: diagram
Text mode diagrams using UTF-8 characters and fancy colors
Papers that mentioned: 20
pypi: cftool
Get inputs and outputs from Codeforces and others online judges
Papers that mentioned: 20
cran: hexbin
Hexagonal Binning Routines
Papers that mentioned: 20
pypi: Chameleon
Fast HTML/XML Template Compiler.
Papers that mentioned: 20
cran: png
Read and write PNG images
Papers that mentioned: 20
cran: growthcurver
Simple Metrics to Summarize Growth Curves
Papers that mentioned: 20
pypi: psychtoolbox
Pieces of Psychtoolbox-3 ported to CPython.
Papers that mentioned: 20
cran: Gmisc
Descriptive Statistics, Transition Plots, and More
Papers that mentioned: 20
pypi: Snowball
Investment strategy backtesting tool
Papers that mentioned: 20
bioconductor: IPO
Automated Optimization of XCMS Data Processing parameters
Papers that mentioned: 20
pypi: LigParGen
Python script to provide BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.
Papers that mentioned: 20
cran: seg
Measuring Spatial Segregation
Papers that mentioned: 20
pypi: recon
Recon is a Trigger-based replacement for RANCID.
Papers that mentioned: 20
cran: DiscriMiner
Tools of the Trade for Discriminant Analysis
Papers that mentioned: 20
cran: argparse
Command Line Optional and Positional Argument Parser
Papers that mentioned: 20
cran: RPMM
Recursively Partitioned Mixture Model
Papers that mentioned: 20
cran: diagram
Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
Papers that mentioned: 20
pypi: rsm
Let's simplify things for real, shall we?
Papers that mentioned: 20
pypi: RUST
Unit step transformation of Ribo-Seq data
Papers that mentioned: 20
pypi: labelImg
LabelImg is a graphical image annotation tool and label object bounding boxes in images
Papers that mentioned: 20
pypi: hybrid
hybrid tools set
Papers that mentioned: 20
pypi: SMBL
SnakeMake Bioinformatics Library.
Papers that mentioned: 20
cran: overlap
Estimates of Coefficient of Overlapping for Animal Activity Patterns
Papers that mentioned: 20
pypi: Brat
Simple framework for creating REST APIs
Papers that mentioned: 20
pypi: boa
Integrated suite for beam optics and analysis
Papers that mentioned: 20
pypi: algorithm
Model an algorithm as a list of functions.
Papers that mentioned: 20
cran: corHMM
Hidden Markov Models of Character Evolution
Papers that mentioned: 20
cran: compareGroups
Descriptive Analysis by Groups
Papers that mentioned: 20
cran: COCONUT
COmbat CO-Normalization Using conTrols (COCONUT)
Papers that mentioned: 20
pypi: bespoke

Papers that mentioned: 20
cran: clustsig
Significant Cluster Analysis
Papers that mentioned: 20
cran: fs
Cross-Platform File System Operations Based on 'libuv'
Papers that mentioned: 20
pypi: Batman
A deployment toolbelt
Papers that mentioned: 20
cran: miceadds
Some Additional Multiple Imputation Functions, Especially for 'mice'
Papers that mentioned: 20
cran: ANOM
Analysis of Means
Papers that mentioned: 20
cran: quadprog
Functions to Solve Quadratic Programming Problems
Papers that mentioned: 20
pypi: platinum
Frequently used google chrome commands mappings. A User-Agent generator. All for automation.
Papers that mentioned: 20