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.

Papers: 10.1371/journal.pcbi.1007664

https://doi.org/10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Published: over 4 years ago

Software Mentions 19

bioconductor: AnnotationHub
Client to access AnnotationHub resources
Papers that mentioned: 39
bioconductor: BiocFileCache
Manage Files Across Sessions
Papers that mentioned: 2
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: ensembldb
Utilities to create and use Ensembl-based annotation databases
Papers that mentioned: 12
bioconductor: fishpond
Fishpond: downstream methods and tools for expression data
Papers that mentioned: 1
bioconductor: GenomicAlignments
Representation and manipulation of short genomic alignments
Papers that mentioned: 134
bioconductor: GenomicFeatures
Conveniently import and query gene models
Papers that mentioned: 141
bioconductor: GenomicRanges
Representation and manipulation of genomic intervals
Papers that mentioned: 323
bioconductor: plyranges
A fluent interface for manipulating GenomicRanges
Papers that mentioned: 8
bioconductor: Rsubread
Mapping, quantification and variant analysis of sequencing data
Papers that mentioned: 331
bioconductor: SummarizedExperiment
SummarizedExperiment container
Papers that mentioned: 52
bioconductor: tximeta
Transcript Quantification Import with Automatic Metadata
Papers that mentioned: 11
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Papers that mentioned: 367
pypi: cwltool
Common workflow language reference implementation
Papers that mentioned: 8
pypi: dammit
dammit!
Papers that mentioned: 14
pypi: PACE
Data Quality of Experimental Data
Papers that mentioned: 13,779
pypi: refget
Python client for refget
Papers that mentioned: 4
pypi: seqrepo
alias for the biocommons.seqrepo package
Papers that mentioned: 2