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/s13059-021-02316-z

https://doi.org/10.1186/s13059-021-02316-z

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Cited by: 24
Author(s): Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd Richmond, Donald J. Johann, Halil Bişğin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee S Basehore, Anne Bergstrom Lucas, Daniel L. Burgess, Daniel Butler, Simon Cawley, Chia Jung Chang, Guangchun Chen, Tao Chen, Yun Ching Chen, Daniel J. Craig, Ángela del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, You-Zeng Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff S. Jasper, Giuseppe Jurman, David P. Kreil, Paweł P. Łabaj, Kevin Lai, Jianying Li, Quan Zhen Li, Yulong Li, Chi Kong Li, Zhichao Liu, Mario Solís-López, Kelci Miclaus, Raymond D. Miller, Vinay Kumar Mittal, Marghoob Mohiyuddin, Carlos Pabón-Peña, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy M. Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Leming Shi, Joshua Xu
Published: over 3 years ago

Software Mentions 10

bioconductor: CODEX
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
Papers that mentioned: 72
bioconductor: CopywriteR
Copy number information from targeted sequencing using off-target reads
Papers that mentioned: 28
cran: ExomeDepth
Calls Copy Number Variants from Targeted Sequence Data
Papers that mentioned: 112
cran: Platypus
Single-Cell Immune Repertoire and Gene Expression Analysis
Papers that mentioned: 218
cran: tmap
Thematic Maps
Papers that mentioned: 88
pypi: bwa
Bwa: Simple Notification Sender(Discord, Slack, Gmail and Telegram)
Papers that mentioned: 989
pypi: CNVkit
Copy number variation toolkit for high-throughput sequencing.
Papers that mentioned: 161
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
pypi: Platypus
A minimal language
Papers that mentioned: 218
pypi: tmap
A topological data analysis framework implementing the TDA Mapper algorithm for population-scale microbiome data analysis
Papers that mentioned: 88