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.

Projects: bioconductor: RiboProfiling

https://packages.ecosyste.ms/registries/bioconductor.org/packages/RiboProfiling

Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
1 version
Latest release: 12 months ago
14,467 downloads total

Papers Mentioning RiboProfiling 11

10.1186/s12864-019-5700-7

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pcbi.1006169

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Cited by: 115
Author(s): Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J N Groen, Thomas H. Gillingwater, Gabriella Viero
Software Mentions: 7
Published: about 6 years ago

10.3390/ijms22094531

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes
Cited by: 4
Author(s): Alexander V. Gopanenko, Alena V. Kolobova, Alexey E. Tupikin, Мarsel R. Kabilov, Alexey A. Malygin, Г. Г. Карпова
Software Mentions: 6
Published: over 3 years ago

10.12688/f1000research.8964.1

RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing
Cited by: 58
Author(s): Alexandra Popa, Kévin Lebrigand, Agnès Paquet, Nicolas Nottet, Karine Robbe-Sermesant, Rainer Waldmann, Pascal Barbry
Software Mentions: 6
Published: over 8 years ago

10.1186/s12934-020-01489-9

Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii
Cited by: 6
Author(s): Troy R Alva, Melanie Riera, J.W. Chartron
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-019-3244-0

DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data
Cited by: 6
Author(s): Henggang Cui, Hailin Hu, Jianyang Zeng, Ting Chen
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-021-04192-7

A tool for analyzing and visualizing ribo-seq data at the isoform level
Cited by: 0
Author(s): Wei Wu, Yi Hong Tsao, Sheng Cian Shiue, Ting Yu Chen, Yan Yuan Tseng, Joseph T. Tseng
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-021-04068-w

RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
Cited by: 2
Author(s): Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O’Brien
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2020.572237

Construction of High-Quality Rice Ribosome Footprint Library
Cited by: 4
Author(s): Xiaoyu Yang, Jie Cui, Bo Song, Yu Yu, Beixin Mo, Lin Liu
Software Mentions: 3
Published: about 4 years ago

10.3389/fonc.2020.622294

LncRNA-Encoded Peptide: Functions and Predicting Methods
Cited by: 47
Author(s): Jiani Xing, Haizhou Liu, Wei Jiang, Lihong Wang
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-42348-x

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming
Cited by: 17
Author(s): Nabeel Ahmed, Pietro Sormanni, Prajwal Ciryam, Michele Vendruscolo, Edward P. O’Brien
Software Mentions: 2
Published: over 5 years ago