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: Repitools
https://packages.ecosyste.ms/registries/bioconductor.org/packages/Repitools
Epigenomic tools
1 version
Latest release: 12 months ago
1 dependent package
67,129 downloads total
Papers Mentioning Repitools 14
10.1186/s13148-019-0795-x
DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysisCited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: almost 5 years ago
10.1186/s13148-019-0651-z
Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progressionCited by: 18
Author(s): Shivani Kamdar, Ruth Isserlin, Theodorus van der Kwast, Alexandre R. Zlotta, Gary D. Bader, Neil Fleshner, Bharati Bapat
Software Mentions: 7
Published: over 5 years ago
10.7554/eLife.05255
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptationCited by: 402
Author(s): Manu Dubin, Pei Zhang, Dong Meng, Marie Stanislas Remigereau, Edward J. Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Géraldine Jean, Bjarni J. Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver Stegle, Richard M. Clark, Magnus Nordborg
Software Mentions: 5
Published: over 9 years ago
10.1186/gb-2014-15-2-r35
BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approachCited by: 26
Author(s): Andrea Riebler, Mirco Menigatti, Jenny Z. Song, Aaron L. Statham, Clare Stirzaker, Nadiya Mahmud, Charles A. Mein, Susan J. Clark, Mark D. Robinson
Software Mentions: 5
Published: almost 11 years ago
10.1186/1471-2164-14-331
Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafishCited by: 32
Author(s): Håvard Aanes, Oľga Østrup, Ingrid S. Andersen, Lars Fredrik Moen, Sinnakaruppan Mathavan, Philippe Collas, Peter Aleström
Software Mentions: 4
Published: over 11 years ago
10.1186/s13148-015-0086-0
Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesisCited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 9 years ago
10.1016/j.febslet.2015.11.027
Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resourceCited by: 12
Author(s): Guillaume Devailly, Anna Mantsoki, Tom Michoel, Anagha Joshi
Software Mentions: 3
Published: almost 9 years ago
10.1186/s40478-018-0519-z
Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injuryCited by: 22
Author(s): Anssi Lipponen, Assam El‐Osta, Antony Kaspi, Mark Ziemann, Ishant Khurana, K N Harikrishnan, Vicente Navarro-Ferrandis, Noora Puhakka, Jussi Paananen, Asla Pitkänen
Software Mentions: 2
Published: over 6 years ago
10.1186/gb-2013-14-9-r98
The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cellsCited by: 44
Author(s): Gonçalo Castelo‐Branco, Paulo Amaral, Pär G. Engström, Samuel Robson, Sueli Marques, Paul Bertone, Tony Kouzarides
Software Mentions: 2
Published: almost 12 years ago
10.1186/s13148-016-0195-4
Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesisCited by: 19
Author(s): Shivani Kamdar, Linh Ho, Ken J. Kron, Ruth Isserlin, Theodorus H. van der Kwast, Alexandre R. Zlotta, Neil Fleshner, Gary D. Bader, Bharati Bapat
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2164-16-S12-S11
MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing dataCited by: 23
Author(s): Wen‐Wei Liao, Ming‐Ren Yen, Evaline Ju, Fei‐Man Hsu, Larry Lam, Pao‐Yang Chen
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0046811
A Global Genome Segmentation Method for Exploration of Epigenetic PatternsCited by: 23
Author(s): Lydia Steiner, Lydia Hopp, Henry Wirth, Joerg Galle, Hans Binder, Sonja J. Prohaska, Thimo Rohlf
Software Mentions: 1
Published: almost 12 years ago
10.1186/s12859-019-3011-2
A model of pulldown alignments from SssI-treated DNA improves DNA methylation predictionCited by: 0
Author(s): B. Moreland, Kenji Oman, Ralf Bundschuh
Software Mentions: 1
Published: about 5 years ago
10.1038/leu.2013.338
Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemiaCited by: 150
Author(s): Mark A. Dawson, Emma Gudgin, Sarah J. Horton, George Giotopoulos, Eshwar Meduri, Samuel Robson, Ester Cannizzaro, Hikari Osaki, Meike Wiese, Sarah Putwain, Chun Yew Fong, Carolyn Grove, Jenny I. O. Craig, Antje Dittmann, David Lugo, Philip D. Jeffrey, Gerard Drewes, K Lee, Lars Bullinger, Rab K. Prinjha, Tony Kouzarides, George S. Vassiliou, Brian J. P. Huntly
Software Mentions: 1
Published: almost 11 years ago