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: pypi: PePr

https://packages.ecosyste.ms/registries/pypi.org/packages/PePr

Peak-calling and Prioritization pipeline for replicated ChIP-Seq data
37 versions
Latest release: about 1 year ago
54 downloads last month

Papers Mentioning PePr 18

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago

10.3390/ijms22115751

Multi-Omics Model Applied to Cancer Genetics
Cited by: 14
Author(s): Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
Software Mentions: 14
Published: over 3 years ago

10.1186/s12974-018-1113-9

Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness
Cited by: 45
Author(s): David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan
Software Mentions: 9
Published: over 6 years ago

10.1186/s12859-019-3090-0

CSA: a web service for the complete process of ChIP-Seq analysis
Cited by: 2
Author(s): Min Li, Li Tang, Fang‐Xiang Wu, Yi Pan, Jianxin Wang
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12859-018-2140-3

iSeg: an efficient algorithm for segmentation of genomic and epigenomic data
Cited by: 9
Author(s): Senthil Balaji Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel Vera, Jane A Dennis, Hank W. Bass, Jinfeng Zhang
Software Mentions: 7
Published: over 6 years ago

10.26508/lsa.201800085

Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Cited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pbio.3000378

Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells
Cited by: 33
Author(s): Yiqin Ma, Daniel J. McKay, Laura Buttitta
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2019.01207

Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus
Cited by: 26
Author(s): Sarah-Anne David, Anaïs Vitorino Carvalho, Coralie Gimonnet, Aurélien Brionne, Christelle Hennequet-Antier, Benoît Piégu, Sabine Crochet, Nathalie Couroussé, Thierry Bordeau, Yves Bigot, Anne Collin, Vincent Coustham
Software Mentions: 5
Published: almost 5 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 -steering
Cited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.31159

ERα promotes murine hematopoietic regeneration through the Ire1α-mediated unfolded protein response
Cited by: 37
Author(s): Richard H. Chapple, Tianyuan Hu, Yung Zu Tseng, L. Liu, Ayumi Kitano, Victor Luu, Kevin A. Hoegenauer, Takao Iwawaki, Qing Li, Daisuke Nakada
Software Mentions: 4
Published: almost 7 years ago

10.18632/oncotarget.14050

Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer
Cited by: 12
Author(s): Yanxiao Zhang, Jie Yu, Vladimir Grachtchouk, Tingting Qin, Carey N. Lumeng, Maureen A. Sartor, Ronald J. Koenig
Software Mentions: 3
Published: almost 8 years ago

10.1093/bioinformatics/btaa960

Fast detection of differential chromatin domains with SCIDDO
Cited by: 7
Author(s): Peter Ebert, Marcel H. Schulz
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13148-020-00965-8

5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers
Cited by: 8
Author(s): Siyu Liu, Marcell Costa de Medeiros, Evan Fernandez, Katie R. Zarins, Raymond G. Cavalcante, Tingting Qin, Gregory T. Wolf, María E. Figueroa, Nisha J. D’Silva, Laura S. Rozek, Maureen A. Sartor
Software Mentions: 3
Published: about 4 years ago

10.1074/jbc.RA119.010080

The role of the histone H3 variant CENPA in prostate cancer
Cited by: 42
Author(s): Anjan K. Saha, Rafael Contreras-Galindo, Yashar S. Niknafs, Matthew K. Iyer, Tingting Qin, Karthik Ramaswamy Padmanabhan, Javed Siddiqui, Monica Palande, Claire Wang, Brian Qian, Elizabeth Ward, Tara Tang, Scott A. Tomlins, Scott D. Gitlin, Maureen A. Sartor, Gilbert S. Omenn, Arul M. Chinnaiyan, David M. Markovitz
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pbio.2004880

METTL3-mediated m6A modification is required for cerebellar development
Cited by: 195
Author(s): Chenxin Wang, Guanshen Cui, Xiu Ying Liu, Kai Xu, Meng Wang, Xinxin Zhang, Liyuan Jiang, Ang Li, Ying Yang, Weiyi Lai, Bao‐Fa Sun, Guibin Jiang, Hailin Wang, Wei‐Min Tong, Wei Li, Xiu‐Jie Wang, Yun‐Gui Yang, Qi Zhou
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-017-3640-7

The Krüppel-like factor 9 cistrome in mouse hippocampal neurons reveals predominant transcriptional repression via proximal promoter binding
Cited by: 31
Author(s): Joseph R. Knoedler, Arasakumar Subramani, Robert J. Denver
Software Mentions: 2
Published: over 7 years ago