bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisPapers that mentioned: 367
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pypi: Archive
Simple library that provides a common interface for extracting zip and tar archives.Papers that mentioned: 363
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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
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cran: MatchIt
Nonparametric Preprocessing for Parametric Causal InferencePapers that mentioned: 358
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bioconductor: Rsubread
Mapping, quantification and variant analysis of sequencing dataPapers that mentioned: 331
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bioconductor: GenomicRanges
Representation and manipulation of genomic intervalsPapers that mentioned: 323
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bioconductor: NOISeq
Exploratory analysis and differential expression for RNA-seq dataPapers that mentioned: 321
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cran: UpSetR
A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting SetsPapers that mentioned: 319
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bioconductor: GEM
GEM: fast association study for the interplay of Gene, Environment and MethylationPapers that mentioned: 317
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pypi: pwr
This program helps you write html pages like documents in word processorsPapers that mentioned: 312
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cran: Modeler
Classes and Methods for Training and Using Binary Prediction ModelsPapers that mentioned: 310
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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
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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
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cran: mclust
Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density EstimationPapers that mentioned: 297
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cran: nnet
Feed-Forward Neural Networks and Multinomial Log-Linear ModelsPapers that mentioned: 296
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cran: INSPIRE
Inferring Shared Modules from Multiple Gene Expression Datasets with Partially Overlapping Gene SetsPapers that mentioned: 296
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pypi: TSA
Papers that mentioned: 293
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pypi: GSA
Python Package to implement Gravitational Search Algorithm. Documentation at:https://github.com/deepanshu1999/GSAPapers that mentioned: 285
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bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataPapers that mentioned: 276
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bioconductor: dada2
Accurate, high-resolution sample inference from amplicon sequencing dataPapers that mentioned: 274
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pypi: SE
A Python stream editor for command-line calls or integration into Python programs.Papers that mentioned: 268
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pypi: Turk
A framework for interfacing applications and devices with the webPapers that mentioned: 261
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bioconductor: EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq dataPapers that mentioned: 261
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cran: AICcmodavg
Model Selection and Multimodel Inference Based on (Q)AIC(c)Papers that mentioned: 261
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bioconductor: GPA
GPA (Genetic analysis incorporating Pleiotropy and Annotation)Papers that mentioned: 260
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pypi: sp
Quickly find out which directories / files are hogging your disk space.Papers that mentioned: 258
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cran: IMAGE
Papers that mentioned: 256
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cran: Rtsne
T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut ImplementationPapers that mentioned: 255
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cran: timeROC
Time-Dependent ROC Curve and AUC for Censored Survival DataPapers that mentioned: 254
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pypi: lattice
A framework for developing data models, including schema development and documentation.Papers that mentioned: 251
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pypi: PREDICT
Predict: a Radiomics Extensive Digital Interchangable Classification Toolkit.Papers that mentioned: 249
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