Packages with Software Mentions in Scientific Papers

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Papers that mentioned: 243

pypi: picard

The next generation MusicBrainz tagger
Papers that mentioned: 243

cran: kmer

Fast K-Mer Counting and Clustering for Biological Sequence Analysis
Papers that mentioned: 240

cran: GLIDE

Global and Individual Tests for Direct Effects
Papers that mentioned: 239

bioconductor: lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Papers that mentioned: 238

cran: SEA

Segregation Analysis
Papers that mentioned: 238

pypi: primer

A primer for prime numbers
Papers that mentioned: 237

cran: primer

Functions and Data for the Book, a Primer of Ecology with R
Papers that mentioned: 237

cran: TAM

Test Analysis Modules
Papers that mentioned: 237

cran: OpenCL

Interface allowing R to use OpenCL
Papers that mentioned: 236

pypi: finder

Command line interface for searching a given pattern in the given directory/file paths
Papers that mentioned: 236

cran: iNEXT

Interpolation and Extrapolation for Species Diversity
Papers that mentioned: 235

cran: spdep

Spatial Dependence: Weighting Schemes, Statistics
Papers that mentioned: 233

pypi: analyzer

python project for finance: realtime data collection, analyze, algorithmic trading
Papers that mentioned: 230

cran: analyzer

Data Analysis and Automated R Notebook Generation
Papers that mentioned: 230

cran: irr

Various Coefficients of Interrater Reliability and Agreement
Papers that mentioned: 228

pypi: lme

Cotação London Metal Exchange
Papers that mentioned: 228

pypi: irr

numpy.irr but works
Papers that mentioned: 228

bioconductor: DEXSeq

Inference of differential exon usage in RNA-Seq
Papers that mentioned: 226

pypi: PSI

Python System Information
Papers that mentioned: 225

pypi: FSA

Finite State Automaton library
Papers that mentioned: 225

cran: FSA

Simple Fisheries Stock Assessment Methods
Papers that mentioned: 225

cran: qgraph

Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
Papers that mentioned: 222

bioconductor: Biostrings

Efficient manipulation of biological strings
Papers that mentioned: 220

pypi: Orange

Orange, a component-based data mining framework.
Papers that mentioned: 219

cran: CAST

'caret' Applications for Spatial-Temporal Models
Papers that mentioned: 219

pypi: Platypus

A minimal language
Papers that mentioned: 218

cran: indicspecies

Relationship Between Species and Groups of Sites
Papers that mentioned: 218

cran: Platypus

Single-Cell Immune Repertoire and Gene Expression Analysis
Papers that mentioned: 218

bioconductor: DiffBind

Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217

cran: MAT

Multidimensional Adaptive Testing
Papers that mentioned: 216

cran: MAP

Multimodal Automated Phenotyping
Papers that mentioned: 215

cran: ggmap

Spatial Visualization with ggplot2
Papers that mentioned: 213

bioconductor: RankProd

Rank Product method for identifying differentially expressed genes with application in meta-analysis
Papers that mentioned: 213

pypi: seqtk

seqtk provides various tools for Sequence.
Papers that mentioned: 213

pypi: image

Django application that provides cropping, resizing, thumbnailing, overlays and masking for images and videos with the ability to set the center of attention,
Papers that mentioned: 212

pypi: ensembl

Ensembl REST API Client
Papers that mentioned: 212

cran: geomorph

Geometric Morphometric Analyses of 2D and 3D Landmark Data
Papers that mentioned: 212

pypi: Imager

A Image Finder Search Engine.
Papers that mentioned: 211

cran: dlnm

Distributed Lag Non-Linear Models
Papers that mentioned: 209

pypi: BioID

A python package for autonomously identifying Bioinformatic file formats.
Papers that mentioned: 208

pypi: Bottleneck

Fast NumPy array functions written in C
Papers that mentioned: 208

cran: lmtest

Testing Linear Regression Models
Papers that mentioned: 208

bioconductor: ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Papers that mentioned: 208

pypi: xgboost

XGBoost Python Package
Papers that mentioned: 207

pypi: shell

A better way to run shell commands in Python.
Papers that mentioned: 207

cran: xgboost

Extreme Gradient Boosting
Papers that mentioned: 207

cran: ecodist

Dissimilarity-Based Functions for Ecological Analysis
Papers that mentioned: 205

bioconductor: SNPRelate

Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Papers that mentioned: 204

cran: caper

Comparative Analyses of Phylogenetics and Evolution in R
Papers that mentioned: 204

pypi: caper

Cromwell Assisted Pipeline ExecutoR
Papers that mentioned: 204

bioconductor: oligo

Preprocessing tools for oligonucleotide arrays
Papers that mentioned: 204

pypi: oligo

UNOFFICIAL Python client for i-DE
Papers that mentioned: 204

pypi: Studio

Web-based administration interface for MapServer
Papers that mentioned: 203

pypi: libsvm

Pre-built LibSVM packages for Python.
Papers that mentioned: 203

cran: dendextend

Extending 'dendrogram' Functionality in R
Papers that mentioned: 201

pypi: Expression

Practical functional programming for Python 3.9+
Papers that mentioned: 200

cran: adehabitatHR

Home Range Estimation
Papers that mentioned: 200

pypi: ViennaRNA

A library for the prediction and comparison of RNA secondary structures.
Papers that mentioned: 200

cran: epiR

Tools for the Analysis of Epidemiological Data
Papers that mentioned: 199

pypi: PIC

图片合成 API
Papers that mentioned: 199

cran: JADE

Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
Papers that mentioned: 198

cran: BGLR

Bayesian Generalized Linear Regression
Papers that mentioned: 197

pypi: Quest

UNKNOWN
Papers that mentioned: 197

pypi: fastx

Just a simple kseq.h binding
Papers that mentioned: 197

pypi: hmmer

HMMER binaries.
Papers that mentioned: 196

pypi: DEA

A simple library for differential expression analysis
Papers that mentioned: 195

pypi: scikit-image

Image processing in Python
Papers that mentioned: 195

cran: DHARMa

Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Papers that mentioned: 194

pypi: 3

Hey
Papers that mentioned: 193

pypi: NEMO

NEMO is a laboratory logistics web application. Use it to schedule reservations, control tool access, track maintenance issues, and more.
Papers that mentioned: 193