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: FME
A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo AnalysisPapers that mentioned: 43
pypi: Escher
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Metabolic PathwaysPapers that mentioned: 43
pypi: bcbio-nextgen
Best-practice pipelines for fully automated high throughput sequencing analysisPapers that mentioned: 43
bioconductor: multiMiR
Integration of multiple microRNA-target databases with their disease and drug associationsPapers that mentioned: 43
pypi: CRISPResso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing dataPapers that mentioned: 43
cran: rfPermute
Estimate Permutation p-Values for Random Forest Importance MetricsPapers that mentioned: 42
cran: adephylo
Exploratory Analyses for the Phylogenetic Comparative MethodPapers that mentioned: 42
bioconductor: genefu
Computation of Gene Expression-Based Signatures in Breast CancerPapers that mentioned: 42
pypi: express
Safely process expressions and templates based on user input.Papers that mentioned: 42
pypi: IsoCor
IsoCor: Isotope Correction for mass spectrometry labeling experimentsPapers that mentioned: 42
cran: LSC
Local Statistical Complexity - Automatic Pattern Discovery in Spatio-Temporal DataPapers that mentioned: 42
pypi: MAnorm
A robust model for quantitative comparison of ChIP-Seq data setsPapers that mentioned: 42
pypi: icoshift
icoshift: A versatile tool for the rapid alignment of 1D NMR spectraPapers that mentioned: 42
cran: sm
Smoothing Methods for Nonparametric Regression and Density EstimationPapers that mentioned: 42
cran: generator
Generate Data Containing Fake Personally Identifiable InformationPapers that mentioned: 42
pypi: MinimPy
MinimPy is a desktop application program for sequential allocation of subjects to treatment groups in clinical trials by using the method of minimisation.Papers that mentioned: 42
pypi: pdb2pqr
Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.Papers that mentioned: 41
pypi: eggnog-mapper
Fast functional annotation of novel sequences using eggNOG orthology assignments.Papers that mentioned: 41
bioconductor: GOSim
Computation of functional similarities between GO terms and gene products; GO enrichment analysisPapers that mentioned: 41
cran: PMCMRplus
Calculate Pairwise Multiple Comparisons of Mean Rank Sums ExtendedPapers that mentioned: 41
pypi: scikit-bio
Data structures, algorithms and educational resources for bioinformatics.Papers that mentioned: 41
bioconductor: apeglm
Approximate posterior estimation for GLM coefficientsPapers that mentioned: 41
cran: ggeffects
Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model OutputsPapers that mentioned: 41
cran: Canopy
Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation SequencingPapers that mentioned: 41
bioconductor: DriverNet
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancerPapers that mentioned: 41
pypi: robustbase
A Python Based Library to Calculate Estimators (Sn, Qn, MAD, IQR)Papers that mentioned: 41
bioconductor: BioNet
Routines for the functional analysis of biological networksPapers that mentioned: 40
cran: NPS
Convenience Functions and Tests for Working With the Net Promoter Score (NPS)Papers that mentioned: 40
cran: BIOMASS
Estimating Aboveground Biomass and Its Uncertainty in Tropical ForestsPapers that mentioned: 40
pypi: BitBucket
Papers that mentioned: 40bioconductor: OmicCircos
High-quality circular visualization of omics dataPapers that mentioned: 40
bioconductor: SIMLR
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)Papers that mentioned: 40
cran: Zelig
Papers that mentioned: 40pypi: SIMLR
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learningPapers that mentioned: 40
cran: pavo
Perceptual Analysis, Visualization and Organization of Spectral Colour DataPapers that mentioned: 39
cran: nFactors
Parallel Analysis and Other Non Graphical Solutions to the Cattell Scree TestPapers that mentioned: 39