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: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisPapers that mentioned: 367
pypi: Archive
Simple library that provides a common interface for extracting zip and tar archives.Papers that mentioned: 363
cran: TESS
Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction EventsPapers that mentioned: 359
cran: MatchIt
Nonparametric Preprocessing for Parametric Causal InferencePapers that mentioned: 358
bioconductor: Rsubread
Mapping, quantification and variant analysis of sequencing dataPapers that mentioned: 331
bioconductor: GenomicRanges
Representation and manipulation of genomic intervalsPapers that mentioned: 323
bioconductor: NOISeq
Exploratory analysis and differential expression for RNA-seq dataPapers that mentioned: 321
cran: UpSetR
A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting SetsPapers that mentioned: 319
bioconductor: GEM
GEM: fast association study for the interplay of Gene, Environment and MethylationPapers that mentioned: 317
pypi: pwr
This program helps you write html pages like documents in word processorsPapers that mentioned: 312
cran: Modeler
Classes and Methods for Training and Using Binary Prediction ModelsPapers that mentioned: 310
pypi: kallisto
The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.Papers that mentioned: 307
pypi: MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.Papers that mentioned: 306
cran: mclust
Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density EstimationPapers that mentioned: 297
cran: nnet
Feed-Forward Neural Networks and Multinomial Log-Linear ModelsPapers that mentioned: 296
cran: INSPIRE
Inferring Shared Modules from Multiple Gene Expression Datasets with Partially Overlapping Gene SetsPapers that mentioned: 296
pypi: GSA
Python Package to implement Gravitational Search Algorithm. Documentation at:https://github.com/deepanshu1999/GSAPapers that mentioned: 285
bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataPapers that mentioned: 276
bioconductor: dada2
Accurate, high-resolution sample inference from amplicon sequencing dataPapers that mentioned: 274
pypi: SE
A Python stream editor for command-line calls or integration into Python programs.Papers that mentioned: 268
cran: AICcmodavg
Model Selection and Multimodel Inference Based on (Q)AIC(c)Papers that mentioned: 261
pypi: Turk
A framework for interfacing applications and devices with the webPapers that mentioned: 261
bioconductor: EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq dataPapers that mentioned: 261
bioconductor: GPA
GPA (Genetic analysis incorporating Pleiotropy and Annotation)Papers that mentioned: 260
pypi: sp
Quickly find out which directories / files are hogging your disk space.Papers that mentioned: 258
cran: IMAGE
Papers that mentioned: 256cran: Rtsne
T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut ImplementationPapers that mentioned: 255
cran: timeROC
Time-Dependent ROC Curve and AUC for Censored Survival DataPapers that mentioned: 254
pypi: lattice
A framework for developing data models, including schema development and documentation.Papers that mentioned: 251