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: almost 2 years ago
54 downloads last month
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Repository Owner:
shawn (user)
Assistant Professor, Westlake University; bioinformatics; epigenomics Academic
Assistant Professor, Westlake University; bioinformatics; epigenomics Academic
Science Score: 100/100
Starting Score: 100 points
Bonuses:
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+20
Academic repository owner
Repository owned by academic institution
Penalties:
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-10
PyPI ecosystem
General-purpose ecosystem -
-10
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Very Likely Science (100)
Papers Mentioning PePr 18
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 5 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: over 5 years ago
10.3390/ijms22115751
Multi-Omics Model Applied to Cancer GeneticsCited by: 14
Author(s): Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
Software Mentions: 14
Published: about 4 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 illnessCited 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 7 years ago
10.1186/s12859-019-3090-0
CSA: a web service for the complete process of ChIP-Seq analysisCited by: 2
Author(s): Min Li, Li Tang, Fang‐Xiang Wu, Yi Pan, Jianxin Wang
Software Mentions: 8
Published: over 5 years ago
10.1186/s12859-018-2140-3
iSeg: an efficient algorithm for segmentation of genomic and epigenomic dataCited 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 7 years ago
10.26508/lsa.201800085
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cellsCited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: about 7 years ago
10.1371/journal.pbio.3000378
Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cellsCited by: 33
Author(s): Yiqin Ma, Daniel J. McKay, Laura Buttitta
Software Mentions: 6
Published: almost 6 years ago
10.3389/fgene.2019.01207
Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken HypothalamusCited 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: over 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 -steeringCited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: almost 9 years ago
10.7554/eLife.31159
ERα promotes murine hematopoietic regeneration through the Ire1α-mediated unfolded protein responseCited 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: over 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 cancerCited 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: over 8 years ago
10.1093/bioinformatics/btaa960
Fast detection of differential chromatin domains with SCIDDOCited by: 7
Author(s): Peter Ebert, Marcel H. Schulz
Software Mentions: 3
Published: over 4 years ago
10.1186/s13148-020-00965-8
5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancersCited 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: over 4 years ago
10.1074/jbc.RA119.010080
The role of the histone H3 variant CENPA in prostate cancerCited 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: about 5 years ago
10.1371/journal.pbio.2004880
METTL3-mediated m6A modification is required for cerebellar developmentCited 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: about 7 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 bindingCited by: 31
Author(s): Joseph R. Knoedler, Arasakumar Subramani, Robert J. Denver
Software Mentions: 2
Published: over 8 years ago