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: 10.1186/s12859-016-1241-0

https://doi.org/10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment

Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Published: about 8 years ago

Software Mentions 19

bioconductor: BiocParallel
Bioconductor facilities for parallel evaluation
Papers that mentioned: 30
bioconductor: Biostrings
Efficient manipulation of biological strings
Papers that mentioned: 220
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: 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: QuasR
Quantify and Annotate Short Reads in R
Papers that mentioned: 30
bioconductor: Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Papers that mentioned: 138
bioconductor: Rsubread
Mapping, quantification and variant analysis of sequencing data
Papers that mentioned: 331
bioconductor: ShortRead
FASTQ input and manipulation
Papers that mentioned: 119
bioconductor: systemPipeR
systemPipeR: workflow management and report generation environment
Papers that mentioned: 27
bioconductor: VariantAnnotation
Annotation of Genetic Variants
Papers that mentioned: 47
bioconductor: VariantTools
Tools for Exploratory Analysis of Variant Calls
Papers that mentioned: 15
cran: BatchJobs
Batch Computing with R
Papers that mentioned: 2
cran: RAP
Reversal Association Pattern
Papers that mentioned: 118
pypi: bcbio-nextgen
Best-practice pipelines for fully automated high throughput sequencing analysis
Papers that mentioned: 43
pypi: MACS
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,233
pypi: Markdown
Python implementation of John Gruber's Markdown.
Papers that mentioned: 14