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: Chicago

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

CHiCAGO: Capture Hi-C Analysis of Genomic Organization
1 version
Latest release: about 1 year ago
14,645 downloads total

Papers Mentioning Chicago 13

10.1186/s13059-018-1598-7

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
Cited by: 38
Author(s): Ramya Raviram, Pedro P. Rocha, Vincent Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau, Jane A. Skok
Software Mentions: 3
Published: almost 6 years ago

10.1093/gigascience/giy162

A near-chromosome-scale genome assembly of the gemsbok (<i>Oryx gazella</i>): an iconic antelope of the Kalahari desert
Cited by: 116
Author(s): Marta Farré, Qiye Li, Yang Zhou, Joana Damas, Leona G. Chemnick, Jaebum Kim, Oliver A. Ryder, Jian Ma, Guojie Zhang, Denis M. Larkin, Harris A. Lewin
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-016-0992-2

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cited by: 330
Author(s): Jonathan Cairns, Paula Freire-Pritchett, Steven W. Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel R. Zerbino, Stefan Schoenfelder, Biola M. Javierre, Cameron S. Osborne, Peter Fraser, Mikhail Spivakov
Software Mentions: 3
Published: over 8 years ago

10.3390/ijerph15050833

Evaluating the Implementation of a Twitter-Based Foodborne Illness Reporting Tool in the City of St. Louis Department of Health
Cited by: 18
Author(s): Jenine K. Harris, Leslie Hinyard, Kate E. Beatty, Joseph E. Hawkins, Elaine O. Nsoesie, Raed Mansour, John S. Brownstein
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.21926

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
Cited by: 123
Author(s): Paula Freire-Pritchett, Stefan Schoenfelder, Csilla Várnai, Steven W. Wingett, Jonathan Cairns, Amanda J. Collier, Raquel García-Vílchez, Mayra Furlan-Magaril, Cameron S. Osborne, Peter Fraser, Peter J. Rugg‐Gunn, Mikhail Spivakov
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btaa288

HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
Cited by: 11
Author(s): Ryo Nakabayashi, Shinichi Morishita
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btz450

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data
Cited by: 17
Author(s): Jonathan Cairns, William R. Orchard, Valeriya Malysheva, Mikhail Spivakov
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009254

Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease
Cited by: 45
Author(s): Wei Wang, Duo Peng, Rodrigo P. Baptista, Yiran Li, Jessica C. Kissinger, Rick L. Tarleton
Software Mentions: 2
Published: almost 4 years ago

10.5005/jp-journals-10018-1231

Does Chicago Classification address Symptom Correlation with High-resolution Esophageal Manometry?
Cited by: 4
Author(s): M Srinivas, Piyush Bawane
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12879-019-3789-6

Procalcitonin, mid-regional proadrenomedullin and C-reactive protein in predicting treatment outcome in community-acquired febrile urinary tract infection
Cited by: 13
Author(s): Janneke E. Stalenhoef, Cees van Nieuwkoop, Darius Cameron Wilson, Willize E. van der Starre, Tanny J. K. van der Reijden, Nathalie M Delfos, Eliane M. S. Leyten, Ted Koster, Hans C Ablij, Johannes Jan Willem van 't Wout, Jaap T. van Dissel
Software Mentions: 1
Published: over 5 years ago

10.1186/s12934-017-0692-y

Direct hydrogen production from dilute-acid pretreated sugarcane bagasse hydrolysate using the newly isolated Thermoanaerobacterium thermosaccharolyticum MJ1
Cited by: 23
Author(s): Binbin Hu, Ming‐Jun Zhu
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1006994

Modern technologies and algorithms for scaffolding assembled genomes
Cited by: 43
Author(s): Jay Ghurye, Mihai Pop
Software Mentions: 1
Published: over 5 years ago

10.1590/0102-6720201700010019

A PICTORIAL PRESENTATION OF ESOPHAGEAL HIGH RESOLUTION MANOMETRY CURRENT PARAMETERS
Cited by: 9
Author(s): Fernanda Marino Lafraia, Fernando A. M. Herbella, Julia R. Kalluf, Marco G. Patti
Software Mentions: 1
Published: over 7 years ago