Packages with Software Mentions in Scientific Papers

pypi: illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.8+).
Papers that mentioned: 22

Very Likely Science (100)

cran: R0

Estimation of R0 and Real-Time Reproduction Number from Epidemics
Papers that mentioned: 22

Very Likely Science (95)

cran: bestglm

Best Subset GLM and Regression Utilities
Papers that mentioned: 22

Very Likely Science (85)

pypi: maple

reliable, scalable, distributed server framework
Papers that mentioned: 22

Very Likely Science (65)

pypi: fcs

A simple, powerful, and open-source time tracker from the command line
Papers that mentioned: 22

Very Likely Science (65)

pypi: calc

A simple module with the basic functions of a calculator and the calculator itself.
Papers that mentioned: 22

Very Likely Science (65)

cran: SVN

Statistically Validated Networks
Papers that mentioned: 22

Very Likely Science (85)

cran: EMMREML

Fitting Mixed Models with Known Covariance Structures
Papers that mentioned: 22

Very Likely Science (85)

pypi: emcee

The Python ensemble sampling toolkit for MCMC
Papers that mentioned: 22

Very Likely Science (100)

pypi: Gentle

Gentle is a help you quickly submit code to the test environment tools.
Papers that mentioned: 22

Very Likely Science (65)

cran: ASSA

Applied Singular Spectrum Analysis (ASSA)
Papers that mentioned: 22

Very Likely Science (93)

bioconductor: RRHO

Inference on agreement between ordered lists
Papers that mentioned: 22

Very Likely Science (90)

cran: OneStep

One-Step Estimation
Papers that mentioned: 22

Very Likely Science (75)

cran: gnm

Generalized Nonlinear Models
Papers that mentioned: 22

Very Likely Science (100)

bioconductor: rbsurv

Robust likelihood-based survival modeling with microarray data
Papers that mentioned: 22

Very Likely Science (100)

cran: corrr

Correlations in R
Papers that mentioned: 22

Very Likely Science (100)

bioconductor: NanoStringDiff

Differential Expression Analysis of NanoString nCounter Data
Papers that mentioned: 22

Very Likely Science (100)

pypi: Scrapy

A high-level Web Crawling and Web Scraping framework
Papers that mentioned: 22

Very Likely Science (100)

bioconductor: EGSEA

Ensemble of Gene Set Enrichment Analyses
Papers that mentioned: 22

Very Likely Science (100)

cran: EMSC

Extended Multiplicative Signal Correction
Papers that mentioned: 22

Very Likely Science (77)

pypi: SANE

Python modules for the SANE and pxc200 modules
Papers that mentioned: 22

Very Likely Science (65)

pypi: d3

A D3.js programming API for python
Papers that mentioned: 22

Very Likely Science (65)

pypi: OSP

Papers that mentioned: 22

Unlikely Science (0)

pypi: ModelBuilder

ODE model builder and simulator
Papers that mentioned: 22

Very Likely Science (80)

pypi: Rails

Rails - python web framework
Papers that mentioned: 22

Very Likely Science (65)

cran: compareC

Compare Two Correlated C Indices with Right-Censored Survival Outcome
Papers that mentioned: 22

Very Likely Science (75)

pypi: PRIM

Patient Rule Induction Method for Python
Papers that mentioned: 22

Very Likely Science (100)

pypi: model

Object Relational Mapper (SQL database wrapper)
Papers that mentioned: 22

Very Likely Science (65)

pypi: stacks

Build scripts, applications and servers using the concept of facilities operating in a stack
Papers that mentioned: 22

Very Likely Science (65)

cran: clinfun

Clinical Trial Design and Data Analysis Functions
Papers that mentioned: 22

Very Likely Science (85)

pypi: MathLab

math algorithms
Papers that mentioned: 22

Very Likely Science (75)

pypi: beagle

Command line client for Hound
Papers that mentioned: 22

Very Likely Science (65)

pypi: jieba

Chinese Words Segmentation Utilities
Papers that mentioned: 22

Very Likely Science (65)

bioconductor: RNASeqPower

Sample size for RNAseq studies
Papers that mentioned: 22

Very Likely Science (83)

pypi: popart

Population based training for Pytorch models.
Papers that mentioned: 22

Very Likely Science (65)

bioconductor: HIBAG

HLA Genotype Imputation with Attribute Bagging
Papers that mentioned: 22

Very Likely Science (100)

pypi: Pluto

Interactive IPython kernel for Jupyter with a built in Vulkan graphics engine
Papers that mentioned: 22

Very Likely Science (95)

pypi: torchvision

image and video datasets and models for torch deep learning
Papers that mentioned: 22

Very Likely Science (100)

cran: survAUC

Estimators of Prediction Accuracy for Time-to-Event Data
Papers that mentioned: 22

Very Likely Science (75)

bioconductor: CancerSubtypes

Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Papers that mentioned: 22

Very Likely Science (100)

bioconductor: RTCGA

The Cancer Genome Atlas Data Integration
Papers that mentioned: 22

Very Likely Science (100)

pypi: QMS

Query Made Simple
Papers that mentioned: 22

Very Likely Science (65)

pypi: Pillow

Python Imaging Library (Fork)
Papers that mentioned: 22

Very Likely Science (100)

pypi: relax

Utilities to make Django and CouchDB play more nicely with one another.
Papers that mentioned: 22

Very Likely Science (65)

pypi: SRGAN

Papers that mentioned: 22

Unlikely Science (0)

cran: MEDITS

Analysis of MEDITS-Like Survey Data
Papers that mentioned: 22

Very Likely Science (85)

bioconductor: RCy3

Functions to Access and Control Cytoscape
Papers that mentioned: 22

Very Likely Science (100)

pypi: mac

Technology agnostic orchestration framework
Papers that mentioned: 22

Very Likely Science (80)

cran: QuasiSeq

Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
Papers that mentioned: 22

Very Likely Science (85)

pypi: gnm

Rock n Rolling MCMC Sampler
Papers that mentioned: 22

Very Likely Science (80)

pypi: chewBBACA

A complete suite for gene-by-gene schema creation and strain identification.
Papers that mentioned: 22

Very Likely Science (100)

cran: ncdf4

Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
Papers that mentioned: 22

Very Likely Science (83)

bioconductor: RTCGAToolbox

A new tool for exporting TCGA Firehose data
Papers that mentioned: 22

Very Likely Science (100)

pypi: Eve

Python REST API for Humans.
Papers that mentioned: 22

Very Likely Science (100)

pypi: Moose

Your manager for endless iterative tasks.
Papers that mentioned: 21

Very Likely Science (65)

pypi: haven

flask's style binary server framework
Papers that mentioned: 21

Likely Science (40)

cran: MF

Mitigated Fraction
Papers that mentioned: 21

Very Likely Science (75)

cran: optimx

Expanded Replacement and Extension of the 'optim' Function
Papers that mentioned: 21

Very Likely Science (75)

pypi: ESP32

Module d'utilisation de la carte esp 32 (IOT)
Papers that mentioned: 21

Very Likely Science (65)

bioconductor: HiTC

High Throughput Chromosome Conformation Capture analysis
Papers that mentioned: 21

Very Likely Science (75)

bioconductor: Pi

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Papers that mentioned: 21

Very Likely Science (100)

bioconductor: RedeR

Interactive visualization and manipulation of nested networks
Papers that mentioned: 21

Very Likely Science (100)

pypi: pam

Papers that mentioned: 21

Very Likely Science (65)

cran: biotools

Tools for Biometry and Applied Statistics in Agricultural Science
Papers that mentioned: 21

Very Likely Science (100)

cran: gprofiler2

Interface to the 'g:Profiler' Toolset
Papers that mentioned: 21

Very Likely Science (75)

cran: hglm

Hierarchical Generalized Linear Models
Papers that mentioned: 21

Very Likely Science (85)

bioconductor: DTA

Dynamic Transcriptome Analysis
Papers that mentioned: 21

Very Likely Science (100)

pypi: fisher

Fast Fisher's Exact Test
Papers that mentioned: 21

Very Likely Science (100)

cran: kableExtra

Construct Complex Table with 'kable' and Pipe Syntax
Papers that mentioned: 21

Very Likely Science (100)

cran: MUS

Monetary Unit Sampling and Estimation Methods, Widely Used in Auditing
Papers that mentioned: 21

Very Likely Science (75)

pypi: ARIC

ARIC: Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data
Papers that mentioned: 21

Very Likely Science (100)

cran: automap

Automatic Interpolation Package
Papers that mentioned: 21

Likely Science (50)

cran: tidybayes

Tidy Data and 'Geoms' for Bayesian Models
Papers that mentioned: 21

Very Likely Science (100)

pypi: EAC

Enhanced Autocorrelation
Papers that mentioned: 21

Very Likely Science (75)

cran: OpenML

Open Machine Learning and Open Data Platform
Papers that mentioned: 21

Very Likely Science (100)

cran: MALDIquantForeign

Import/Export Routines for 'MALDIquant'
Papers that mentioned: 21

Very Likely Science (75)

cran: magick

Advanced Graphics and Image-Processing in R
Papers that mentioned: 21

Very Likely Science (93)

pypi: Top

DaYu message api of Ali
Papers that mentioned: 21

Very Likely Science (65)

cran: DiffCorr

Analyzing and Visualizing Differential Correlation Networks in Biological Data
Papers that mentioned: 21

Very Likely Science (85)

pypi: Monte

Monte - machine learning in pure Python.
Papers that mentioned: 21

Very Likely Science (90)

pypi: magick

C-based Python Interface to ImageMagick
Papers that mentioned: 21

Very Likely Science (65)

pypi: build

A simple, correct Python build frontend
Papers that mentioned: 21

Very Likely Science (65)

cran: DET

Papers that mentioned: 21

Unlikely Science (0)

pypi: by

selection tools
Papers that mentioned: 21

Very Likely Science (65)

bioconductor: limmaGUI

GUI for limma Package With Two Color Microarrays
Papers that mentioned: 21

Very Likely Science (100)

cran: rfUtilities

Random Forests Model Selection and Performance Evaluation
Papers that mentioned: 21

Very Likely Science (95)

bioconductor: CNAnorm

A normalization method for Copy Number Aberration in cancer samples
Papers that mentioned: 21

Very Likely Science (90)

pypi: SPDE

Utilities for geostatistics based on stochastic partial differential equations
Papers that mentioned: 21

Very Likely Science (90)

pypi: frappe

Frappe placeholder package
Papers that mentioned: 21

Very Likely Science (65)

bioconductor: CNTools

Convert segment data into a region by sample matrix to allow for other high level computational analyses.
Papers that mentioned: 21

Very Likely Science (100)

pypi: Canto

Next-gen console RSS/Atom reader
Papers that mentioned: 21

Very Likely Science (65)

cran: AEP

Statistical Modelling for Asymmetric Exponential Power Distribution
Papers that mentioned: 21

Very Likely Science (85)

cran: curl

A Modern and Flexible Web Client for R
Papers that mentioned: 21

Very Likely Science (83)

pypi: XAS

Papers that mentioned: 21

Very Likely Science (65)

pypi: WASH

Wolfram|Alpha interactive shell
Papers that mentioned: 21

Very Likely Science (65)

pypi: PyVCF

Variant Call Format (VCF) parser for Python
Papers that mentioned: 21

Very Likely Science (100)

bioconductor: M3Drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Papers that mentioned: 21

Very Likely Science (100)

pypi: automap

High-performance autoincremented integer-valued mappings.
Papers that mentioned: 21

Very Likely Science (85)

cran: haven

Import and Export 'SPSS', 'Stata' and 'SAS' Files
Papers that mentioned: 21

Very Likely Science (100)

cran: SPRT

Wald's Sequential Probability Ratio Test
Papers that mentioned: 21

Very Likely Science (75)