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: csaw
https://packages.ecosyste.ms/registries/bioconductor.org/packages/csaw
ChIP-Seq Analysis with Windows
1 version
Latest release: about 1 year ago
8 dependent packages
64,512 downloads total
Papers Mentioning csaw 29
10.3389/fonc.2020.00423
Computational Oncology in the Multi-Omics Era: State of the ArtCited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago
10.1186/s13059-020-1929-3
From reads to insight: a hitchhiker’s guide to ATAC-seq data analysisCited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago
10.15252/emmm.202012640
Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumorCited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: almost 4 years ago
10.1186/s12859-015-0683-0
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C dataCited by: 172
Author(s): Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 14
Published: about 9 years ago
10.1186/s13072-020-00342-y
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretationCited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 years ago
10.1186/s13059-018-1484-3
CTCF maintains regulatory homeostasis of cancer pathwaysCited by: 39
Author(s): Sarah J. Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C. Marioni, Duncan T. Odom
Software Mentions: 14
Published: over 6 years ago
10.7717/peerj.1981
DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studiesCited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 8 years ago
10.1186/s13059-019-1716-1
A practical guide to methods controlling false discoveries in computational biologyCited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 5 years ago
10.1038/s41388-018-0450-6
The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progressionCited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: about 6 years ago
10.7554/eLife.69937
CLAMP and Zelda function together to promote Drosophila zygotic genome activationCited by: 33
Author(s): Jianan Duan, Leila E. Rieder, Megan M Colonnetta, Annie Huang, Mary Mckenney, Scott Watters, Girish Deshpande, William T. Jordan, Nicolas L. Fawzi, Erica Larschan
Software Mentions: 8
Published: over 3 years ago
10.1186/s12915-019-0726-5
Multi-species annotation of transcriptome and chromatin structure in domesticated animalsCited by: 80
Author(s): Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kévin Muret, Diane Esquerré, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cédric Cabau, Elisa Crisci, Sophie Dhorne–Pollet, Françoise Drouet, Thomas Faraut, Ignacio González, Adeline Goubil, Sonia Lacroix‐Lamandé, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaëlle Momal-Leisenring, Florence Mompart, Pascale Quéré, David Robelin, Magali San Cristobal, Gwenola Tosser‐Klopp, Silvia Vincent‐Naulleau, Stéphane Fabre, Marie-Hélène Pinard van der Laan, Christophe Klopp, Michèle Tixier‐Boichard, Hervé Acloque, Sandrine Lagarrigue, Elisabetta Giuffra
Software Mentions: 8
Published: almost 5 years ago
10.1371/journal.pone.0251032
Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivationCited by: 2
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 8
Published: over 3 years ago
10.1186/s13072-016-0064-6
Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencingCited by: 59
Author(s): Andrew Keniry, Linden J. Gearing, Natasha Jansz, Joy Liu, Aliaksei Z. Holik, Peter Hickey, Sarah Kinkel, Darcy Moore, Kelsey Breslin, Kelan Chen, Ruijie Liu, Chris Phillips, Miha Pakusch, Christine Biben, Julie Sheridan, Benjamin T. Kile, Catherine Carmichael, Matthew E. Ritchie, Douglas J. Hilton, Marnie E. Blewitt
Software Mentions: 8
Published: over 8 years ago
10.3389/fgene.2021.664654
Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in CancerCited by: 0
Author(s): Qi Wang, Yonghe Wu, Tim Vorberg, Roland Eils, Carl Herrmann
Software Mentions: 8
Published: over 3 years ago
10.1186/s12885-020-06777-6
The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancersCited by: 11
Author(s): Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson, Giancarlo Marra
Software Mentions: 7
Published: over 4 years ago
10.12688/f1000research.7016.2
From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq dataCited by: 16
Author(s): Aaron T. L. Lun
Software Mentions: 7
Published: almost 9 years ago
10.1371/journal.ppat.1009567
ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infectionCited by: 7
Author(s): Joseph M Cabral, Camille H. Cushman, Catherine Sodroski, David M. Knipe
Software Mentions: 6
Published: over 3 years ago
10.1242/jcs.259051
The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcriptionCited by: 0
Author(s): David Z. Kochan, Julia S. P. Mawer, Jennifer Massen, Kiril Tishinov, Swati Parekh, Martin Graef, Anne Spang, Peter Tessarz
Software Mentions: 6
Published: over 3 years ago
10.15252/msb.20199156
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liverCited by: 19
Author(s): Vanessa Dubois, Céline Gheeraert, Wouter Vankrunkelsven, Julie Dubois-Chevalier, Hélène Dehondt, Marie Bobowski-Gérard, Manjula Vinod, Francesco Paolo Zummo, Fabian Güiza, Maheul Ploton, Emilie Dorchies, Laurent Pineau, Alexis Boulinguiez, Emmanuelle Vallez, Eloïse Woitrain, Eric Baugé, Fanny Lalloyer, Christian Duhem, Nabil Rabhi, Ronald E. van Kesteren, Cheng Ming Chiang, Steve Lancel, Hélène Duez, Jean-Sébastien Annicotte, Réjane Paumelle, Ilse Vanhorebeek, Greet Van den Berghe, Bart Staels, Philippe Lefèbvre, Jérôme Eeckhoute
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.ppat.1009346
Epigenomic characterization of latent HIV infection identifies latency regulating transcription factorsCited by: 27
Author(s): Stuart R. Jefferys, Samuel D. Burgos, Jackson J Peterson, Sara R. Selitsky, Anne-Marie W. Turner, Lindsey I. James, Yi-Hsuan Tsai, Alisha R. Coffey, David M. Margolis, Joel S. Parker, Edward P. Browne
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-016-1248-6
Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steeringCited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: about 8 years ago
10.1093/gigascience/giy080
A workflow for simplified analysis of ATAC-cap-seq data in RCited by: 5
Author(s): Ram Krishna Shrestha, Pingtao Ding, Jonathan D. G. Jones, Dan MacLean
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-018-4479-2
Consequences of early life stress on genomic landscape of H3K4me3 in prefrontal cortex of adult miceCited by: 20
Author(s): Nikita I. Ershov, Natalia P. Bondar, Arina A. Lepeshko, Vasiliy V. Reshetnikov, Julia A. Ryabushkina, T. I. Merkulova
Software Mentions: 3
Published: almost 7 years ago
10.7554/eLife.34970
SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevityCited by: 17
Author(s): Wenke Wang, Amaresh Chaturbedi, Minghui Wang, Serim An, Velayudhan Satheeja Santhi, Siu Sylvia Lee
Software Mentions: 3
Published: over 6 years ago
10.1186/s13072-020-00365-5
Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequencesCited by: 23
Author(s): Jingyi Tang, Scott A. Chisholm, Lee M. Yeoh, Paul R. Gilson, Anthony T. Papenfuss, Karen P. Day, Michaela Petter, Michael Duffy
Software Mentions: 3
Published: almost 4 years ago
10.1242/dev.122077
Repression of <i>Igf1</i> expression by Ezh2 prevents basal cell differentiation in the developing lungCited by: 48
Author(s): Laura A. Galvis, Aliaksei Z. Holik, Kieran M. Short, Julie Pasquet, Aaron T. L. Lun, Marnie E. Blewitt, Ian Smyth, Matthew E. Ritchie, Marie Liesse Asselin-Labat
Software Mentions: 2
Published: almost 10 years ago
10.3389/fmicb.2018.01416
Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coliCited by: 6
Author(s): Christina Gabrielsen, Finn Drabløs, Kjersti Haugum, Jan Egil Afset
Software Mentions: 2
Published: over 6 years ago
10.1186/s13104-018-3633-x
The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experimentsCited by: 3
Author(s): Daniel Wiegreffe, Lydia Müller, Jens Steuck, Dirk Zeckzer, Peter F. Stadler
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-019-5472-0
Genome-wide analysis of epigenetic dynamics across human developmental stages and tissuesCited by: 3
Author(s): Xia Zhang, Yanglan Gan, Guobing Zou, Jihong Guan, Shuigeng Zhou
Software Mentions: 2
Published: over 5 years ago