# 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: ABAEnrichment

Papers that mentioned: 2##### bioconductor: ABarray

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.Papers that mentioned: 4

##### bioconductor: ABSSeq

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differencesPapers that mentioned: 7

##### bioconductor: ACE

Absolute Copy Number Estimation from Low-coverage Whole Genome SequencingPapers that mentioned: 478

##### bioconductor: aCGH

Classes and functions for Array Comparative Genomic Hybridization dataPapers that mentioned: 32

##### bioconductor: ACME

Algorithms for Calculating Microarray Enrichment (ACME)Papers that mentioned: 63

##### bioconductor: affycomp

Graphics Toolbox for Assessment of Affymetrix Expression MeasuresPapers that mentioned: 13

##### bioconductor: affycoretools

Functions useful for those doing repetitive analyses with Affymetrix GeneChipsPapers that mentioned: 36

##### bioconductor: affyILM

Linear Model of background subtraction and the Langmuir isothermPapers that mentioned: 2

##### bioconductor: affyPara

Papers that mentioned: 2##### bioconductor: AffyRNADegradation

Analyze and correct probe positional bias in microarray data due to RNA degradationPapers that mentioned: 6

##### bioconductor: AgiMicroRna

Processing and Differential Expression Analysis of Agilent microRNA chipsPapers that mentioned: 37

##### bioconductor: AIMS

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular SubtypePapers that mentioned: 77

##### bioconductor: ALDEx2

Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountPapers that mentioned: 136

##### bioconductor: AlphaBeta

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plantsPapers that mentioned: 7

##### bioconductor: ALPS

Papers that mentioned: 18##### bioconductor: alsace

Papers that mentioned: 1##### bioconductor: altcdfenvs

alternative CDF environments (aka probeset mappings)Papers that mentioned: 5

##### bioconductor: AMARETTO

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized RegressionPapers that mentioned: 5

##### bioconductor: ANCOMBC

Microbiome differential abudance and correlation analyses with bias correctionPapers that mentioned: 2

##### bioconductor: AneuFinder

Analysis of Copy Number Variation in Single-Cell-Sequencing DataPapers that mentioned: 16

##### bioconductor: annmap

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.Papers that mentioned: 5

##### bioconductor: AnnotationDbi

Manipulation of SQLite-based annotations in BioconductorPapers that mentioned: 73

##### bioconductor: AnnotationFilter

Facilities for Filtering Bioconductor Annotation ResourcesPapers that mentioned: 1

##### bioconductor: AnnotationForge

Tools for building SQLite-based annotation data packagesPapers that mentioned: 11

##### bioconductor: annotationTools

Annotate microarrays and perform cross-species gene expression analyses using flat file databasesPapers that mentioned: 3

##### bioconductor: annotatr

Annotation of Genomic Regions to Genomic AnnotationsPapers that mentioned: 15

##### bioconductor: anota2seq

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seqPapers that mentioned: 8

##### bioconductor: apComplex

Estimate protein complex membership using AP-MS protein dataPapers that mentioned: 2

##### bioconductor: apeglm

Approximate posterior estimation for GLM coefficientsPapers that mentioned: 41

##### bioconductor: aroma.light

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data TypesPapers that mentioned: 4

##### bioconductor: ArrayExpress

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSetPapers that mentioned: 1,962

##### bioconductor: ArrayExpressHTS

ArrayExpress High Throughput Sequencing Processing PipelinePapers that mentioned: 7

##### bioconductor: arrayMvout

multivariate outlier detection for expression array QAPapers that mentioned: 3

##### bioconductor: arrayQualityMetrics

Quality metrics report for microarray data setsPapers that mentioned: 190

##### bioconductor: ARRmNormalization

Adaptive Robust Regression normalization for Illumina methylation dataPapers that mentioned: 1

##### bioconductor: ASICS

Automatic Statistical Identification in Complex SpectraPapers that mentioned: 10

##### bioconductor: ASSET

An R package for subset-based association analysis of heterogeneous traits and subtypesPapers that mentioned: 72

##### bioconductor: ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)Papers that mentioned: 54

##### bioconductor: attract

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor LandscapePapers that mentioned: 1

##### bioconductor: AUCell

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Papers that mentioned: 45

##### bioconductor: autonomics

Generifying and intuifying cross-platform omics analysisPapers that mentioned: 6

##### bioconductor: BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomesPapers that mentioned: 1

##### bioconductor: BAC

Papers that mentioned: 14##### bioconductor: bacon

Controlling bias and inflation in association studies using the empirical null distributionPapers that mentioned: 4

##### bioconductor: BADER

Bayesian Analysis of Differential Expression in RNA Sequencing DataPapers that mentioned: 4

##### bioconductor: ballgown

Flexible, isoform-level differential expression analysisPapers that mentioned: 21

##### bioconductor: baySeq

Empirical Bayesian analysis of patterns of differential expression in count dataPapers that mentioned: 139

##### bioconductor: BBCAnalyzer

BBCAnalyzer: an R/Bioconductor package for visualizing base countsPapers that mentioned: 1

##### bioconductor: BCRANK

Predicting binding site consensus from ranked DNA sequencesPapers that mentioned: 6

##### bioconductor: beadarray

Quality assessment and low-level analysis for Illumina BeadArray dataPapers that mentioned: 94

##### bioconductor: beadarraySNP

Normalization and reporting of Illumina SNP bead arraysPapers that mentioned: 3

##### bioconductor: BEARscc

BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)Papers that mentioned: 2

##### bioconductor: BgeeDB

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontologyPapers that mentioned: 4

##### bioconductor: BiGGR

Constraint based modeling in R using metabolic reconstruction databasesPapers that mentioned: 4

##### bioconductor: bigmelon

Illumina methylation array analysis for large experimentsPapers that mentioned: 7

##### bioconductor: bioassayR

Cross-target analysis of small molecule bioactivityPapers that mentioned: 1