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: CSAR

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

Statistical tools for the analysis of ChIP-seq data
1 version
Latest release: about 1 year ago
37,330 downloads total

Papers Mentioning CSAR 15

N<sup>6</sup>‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
Cited by: 35
Author(s): Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. García, Eric Lyons, Mark A. Beilstein, Brian D. Gregory
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2229-14-29

Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor
Cited by: 76
Author(s): Martiniano María Ricardi, Ricardo Mendoza González, Silin Zhong, Pía Guadalupe Domínguez, Tomás Duffy, Pablo Turjanski, Juan D. Salgado Salter, Karina Alleva, Fernando Carrari, James J. Giovannoni, José M. Estevez, Norberto D. Iusem
Software Mentions: 4
Published: almost 11 years ago

10.1186/1746-4811-7-11

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
Cited by: 60
Author(s): Jose M. Muiño, Kerstin Kaufmann, Roeland Chj van Ham, Gerco C. Angenent, Paweł Krajewski
Software Mentions: 3
Published: almost 14 years ago

10.1038/sdata.2015.10

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
Cited by: 48
Author(s): Serdar Turkarslan, Eliza J.R. Peterson, Tige R. Rustad, K Minch, David J Reiss, Robert Morrison, Shuyi Ma, Nathan D. Price, David R. Sherman, Nitin S. Baliga
Software Mentions: 3
Published: over 9 years ago

10.1186/gb-2014-15-1-r3

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
Cited by: 76
Author(s): Ian M. Silverman, Liancheng Fan, A Vinogradov Alexander, Loyal A. Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmolb.2020.601065

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features
Cited by: 14
Author(s): Stefan Holderbach, Lukas Adam, B. Jayaram, Rebecca C. Wade, Goutam Mukherjee
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-5302-9

Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities
Cited by: 18
Author(s): Teresa Mohr, Habibu Aliyu, Raphael Kuchlin, Michaela Zwick, Don A. Cowan, Anke Neumann, Pieter De Maayer
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0085678

istar: A Web Platform for Large-Scale Protein-Ligand Docking
Cited by: 88
Author(s): Hongjian Li, Kwong‐Sak Leung, Pedro J. Ballester, Man‐Hon Wong
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0067536

Towards Ligand Docking Including Explicit Interface Water Molecules
Cited by: 58
Author(s): Gordon Lemmon, Jens Meiler
Software Mentions: 2
Published: over 11 years ago

10.3390/molecules190710150

Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design
Cited by: 152
Author(s): Sam Z. Grinter, Xiaoqin Zou
Software Mentions: 1
Published: over 10 years ago

10.1128/MRA.00307-21

Draft Genome Sequences of <i>Legionella</i> Presumptive Novel Species Isolated during Environmental Surveillance in Artificial Water Systems
Cited by: 4
Author(s): Luna Girolamini, Silvano Salaris, Massimiliano Orsini, Maria Rosaria Pascale, Marta Mazzotta, Antonella Grottola, Sandra Cristino
Software Mentions: 1
Published: over 3 years ago

10.1007/s10822-015-9846-3

Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock
Cited by: 41
Author(s): Ann E. Cleves, Ajay N. Jain
Software Mentions: 1
Published: over 9 years ago

10.1186/s12918-018-0654-y

Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements
Cited by: 8
Author(s): Kun-Tze Chen, Hsin-Ting Shen, Chin Lung Lu
Software Mentions: 1
Published: almost 6 years ago

10.3390/s17081705

Preliminary Assessment of Wind and Wave Retrieval from Chinese Gaofen-3 SAR Imagery
Cited by: 54
Author(s): Weizeng Shao, Yexin Sheng, Jian Sun
Software Mentions: 1
Published: over 7 years ago

10.3390/s19224920

Analysis of the Azimuth Ambiguity and Imaging Area Restriction for Circular SAR Based on the Back-Projection Algorithm
Cited by: 4
Author(s): Bang Du, Xiaolan Qiu, Lizhen Huang, Songlin Lei, Bin Lei, Chibiao Ding
Software Mentions: 1
Published: almost 5 years ago