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: pyGenomeTracks

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

Command-line tool to make beautiful and reproducible genome browser snapshots
16 versions
Latest release: almost 2 years ago
647 downloads last month

Papers Mentioning pyGenomeTracks 20

10.1186/s13059-020-02049-5

Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping
Cited by: 13
Author(s): Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B. Fraser, Thomas Quertermous
Software Mentions: 7
Published: over 4 years ago

10.1093/gigascience/giaa137

Long-read assembly of the Brassica napus reference genome Darmor-bzh
Cited by: 50
Author(s): Mathieu Rousseau‐Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Régine Delourme, Gwenaëlle Deniot, Stéfan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, Anne‐Marie Chèvre, Jean‐Marc Aury
Software Mentions: 6
Published: about 4 years ago

10.15252/msb.202110272

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
Cited by: 32
Author(s): Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, G. Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-020-02216-8

Histone modifications during the life cycle of the brown alga Ectocarpus
Cited by: 21
Author(s): Simon Bourdareau, Leïla Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho, J. Mark Cock
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pgen.1009691

Induction of a chromatin boundary in vivo upon insertion of a TAD border
Cited by: 11
Author(s): Andréa Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodríguez-Carballo
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.63036

Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants
Cited by: 5
Author(s): J. Roman Arguello, Liliane Abuin, Jan Armida, Kaan Mika, Phing Chian Chai, Richard Benton
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-021-02334-x

The impact of cell type and context-dependent regulatory variants on human immune traits
Cited by: 27
Author(s): Zepeng Mu, Wei Wei, Benjamin Jung Fair, Jinlin Miao, Ping Zhu, Yang Li
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-97158-x

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
Cited by: 3
Author(s): Zack Saud, Matthew D. Hitchings, Tariq M. Butt
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00250-20

Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters
Cited by: 16
Author(s): Jessica M. Vera, Indro Neil Ghosh, Yaoping Zhang, Alex S. Hebert, Joshua J. Coon, Robert Landick
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02063-7

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
Cited by: 57
Author(s): Yonghao Sun, Liang Dong, Ying Zhang, Dazhen Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li, Fang Yang
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0232332

Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data
Cited by: 1
Author(s): Ignacio J. Tripodi, Murad Chowdhury, Margaret Gruca, Robin D. Dowell
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-69443-8

AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq
Cited by: 0
Author(s): Laura Arrigoni, F. Ferrari, Juliane Weller, Chiara Bella, Ulrike Bönisch, Thomas Manke
Software Mentions: 3
Published: over 4 years ago

10.1093/bioinformatics/btz436

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Cited by: 92
Author(s): Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon P. Ryan, Thomas Manke
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12020239

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
Cited by: 7
Author(s): Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
Software Mentions: 3
Published: almost 4 years ago

10.1093/g3journal/jkaa005

FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type-specific profiling of protein–DNA interactions in Drosophila melanogaster
Cited by: 5
Author(s): Gabriel Aughey, Caroline Delandre, John P D McMullen, Tony D. Southall, Owen J. Marshall
Software Mentions: 2
Published: about 4 years ago

10.1093/bioinformatics/btaa692

pyGenomeTracks: reproducible plots for multivariate genomic datasets
Cited by: 179
Author(s): Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn Grüning, Fidel Ramírez, Thomas Manke
Software Mentions: 2
Published: over 4 years ago

10.1016/j.cub.2021.01.071

Stem cell niche organization in the Drosophila ovary requires the ECM component Perlecan
Cited by: 16
Author(s): Alfonsa Díaz-Torres, Alicia E. Rosales-Nieves, J. R. A. Pearson, Carmen Santa-Cruz Mateos, Miriam Marín-Menguiano, Owen J. Marshall, Andrea H. Brand, Acaimo González-Reyes
Software Mentions: 1
Published: over 3 years ago

10.3390/ph14050457

Genetic and Epigenetic Alterations of CDH1 Regulatory Regions in Hereditary and Sporadic Gastric Cancer
Cited by: 11
Author(s): Gianluca Tedaldi, Chiara Molinari, Celina São José, Rita Barbosa-Matos, Ana André, Rita Danesi, Valentina Arcangeli, Mila Ravegnani, Luca Saragoni, Paolo Morgagni, Francesca Rebuzzi, Matteo Canale, Sara Pignatta, Elisa Ferracci, Giovanni Martinelli, Guglielmina Nadia Ranzani, Carla Oliveira, Daniele Calistri, Paola Ulivi
Software Mentions: 1
Published: over 3 years ago

10.1128/mSystems.00181-21

One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE)
Cited by: 15
Author(s): Xiaoyan Jing, Yanhai Gong, Teng Xu, Yu Meng, Xiao Han, Xiaolu Su, Jianmei Wang, Yicai Ji, Yuandong Li, Zhilong Jia, Bo Ma, Jian Xu
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.120.401785

Maintenance of Cell Fate by the Polycomb Group Gene Sex Combs Extra Enables a Partial Epithelial Mesenchymal Transition inDrosophila
Cited by: 0
Author(s): Grace Jefferies, Jason Somers, Isabelle Lohrey, Vishal Chaturvedi, Jacob Calabria, Owen J. Marshall, Tony D. Southall, Robert Saint, Michael J. Murray
Software Mentions: 1
Published: about 4 years ago