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/s13059-021-02349-4

https://doi.org/10.1186/s13059-021-02349-4

PEPPRO: quality control and processing of nascent RNA profiling data

Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Published: over 3 years ago

Software Mentions 14

cran: fasta
Fast Adaptive Shrinkage/Thresholding Algorithm
Papers that mentioned: 848
cran: pepr
Reading Portable Encapsulated Projects
Papers that mentioned: 1
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
pypi: fasta
The fasta python package enables you to deal with biological sequence files easily.
Papers that mentioned: 848
pypi: flash
Fast tool
Papers that mentioned: 23
pypi: index
Index System
Papers that mentioned: 11
pypi: looper
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
Papers that mentioned: 2
pypi: numpy
Fundamental package for array computing in Python
Papers that mentioned: 832
pypi: pandas
Powerful data structures for data analysis, time series, and statistics
Papers that mentioned: 640
pypi: pararead
Parallel processing of sequencing reads
Papers that mentioned: 1
pypi: picard
The next generation MusicBrainz tagger
Papers that mentioned: 243
pypi: rb
rb, the redis blaster
Papers that mentioned: 13
pypi: refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file
Papers that mentioned: 3
pypi: seqtk
seqtk provides various tools for Sequence.
Papers that mentioned: 213