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: PyVCF

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

Variant Call Format (VCF) parser for Python
22 versions
Latest release: over 8 years ago
10 dependent packages
64,206 downloads last month

Papers Mentioning PyVCF 21

Phenotype inference in an Escherichia coli strain panel
Cited by: 36
Author(s): Marco Galardini, Alexandra Koumoutsi, Lucía Herrera-Domínguez, Juan Antonio Cordero Varela, Anja Telzerow, Omar Wagih, Morgane Wartel, Olivier Clermont, Erick Denamur, Athanasios Typas, Pedro Beltrão
Software Mentions: 8
Published: almost 7 years ago

10.1534/g3.117.300152

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)
Cited by: 4
Author(s): Venkat Talla, Faheema Kalsoom, Daria Shipilina, И. М. Марова, Niclas Backström
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pgen.1008055

Loss of function mutations in essential genes cause embryonic lethality in pigs
Cited by: 38
Author(s): Martijn F.L. Derks, Arne B. Gjuvsland, Mirte Bosse, Marcos S. Lopes, Maren van Son, B. Harlizius, Beatrice Tan, Hanne Hamland, Eli Grindflek, Martien A. M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1007661

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome
Cited by: 29
Author(s): Martijn F.L. Derks, Marcos S. Lopes, Mirte Bosse, Ole Madsen, Bert Dibbits, B. Harlizius, M.A.M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: about 6 years ago

10.1186/s13742-016-0131-8

Gigwa—Genotype investigator for genome-wide analyses
Cited by: 18
Author(s): Guilhem Sempéré, Philippe Florian, Alexis Dereeper, Manuel Ruiz, Gautier Sarah, Pierre Larmande
Software Mentions: 5
Published: over 8 years ago

10.1093/gigascience/giaa097

Machado: Open source genomics data integration framework
Cited by: 3
Author(s): Maurício de Alvarenga Mudadu, Adhemar Zerlotini
Software Mentions: 5
Published: about 4 years ago

10.1002/ece3.2782

Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff (Phylloscopus collybita abietinus/tristis) hybrid zone
Cited by: 18
Author(s): Daria Shipilina, Maksym Serbyn, В. В. Иваницкий, И. М. Марова, Niclas Backström
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-017-1985-1

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data
Cited by: 6
Author(s): Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck, Geert Vandeweyer
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-14-356

Processing genome scale tabular data with wormtable
Cited by: 11
Author(s): Jerome Kelleher, Rob W. Ness, Daniel L. Halligan
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12711-018-0390-1

A survey of functional genomic variation in domesticated chickens
Cited by: 25
Author(s): Martijn F.L. Derks, Hendrik‐Jan Megens, Mirte Bosse, J. Visscher, Katrijn Peeters, M.C.A.M. Bink, Addie Vereijken, Christian Groß, Dick de Ridder, Marcel J. T. Reinders, Martien A. M. Groenen
Software Mentions: 2
Published: over 6 years ago

10.1186/s12936-021-03788-x

Using deep learning to identify recent positive selection in malaria parasite sequence data
Cited by: 10
Author(s): Wouter Deelder, Ernest Diez Benavente, Jody Phelan, Emilia Mańko, Susana Campino, Luigi Palla, Taane G. Clark
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0198419

Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes
Cited by: 6
Author(s): Bartosz Czech, Magdalena Frąszczak, Magda Mielczarek, Joanna Szyda
Software Mentions: 2
Published: over 6 years ago

10.1093/database/baw104

TMC-SNPdb: an Indian germline variant database derived from whole exome sequences
Cited by: 12
Author(s): Pawan Upadhyay, Nilesh Gardi, Sanket Desai, Bikram Sahoo, Ankita Singh, Trupti Togar, Prajish Iyer, Ratnam Prasad, Pratik Chandrani, Sudeep Gupta, Amit Dutt
Software Mentions: 1
Published: almost 9 years ago

10.1080/21505594.2019.1597496

Differential immune responses of C57BL/6 mice to infection bySalmonella entericaserovar Typhimurium strain SL1344, CVCC541 and CMCC50115
Cited by: 14
Author(s): Wang Shao, Jianwei Huang, Zhexi Liu, Mengyao Wang, Bingkun Zhang, Zhengxing Lian, Yuming Guo, Hongbing Han
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0141105

Virtual Pharmacist: A Platform for Pharmacogenomics
Cited by: 10
Author(s): Ronghai Cheng, Rufina Leung, Yao Chen, Yidan Pan, Yin Tong, Zhoufang Li, Ning Liu, Xuefeng B. Ling, Jiankui He
Software Mentions: 1
Published: about 9 years ago

10.1038/s41421-018-0069-3

Repurposing CRISPR-Cas12b for mammalian genome engineering
Cited by: 168
Author(s): Fei Teng, Tongtong Cui, Guihai Feng, Lu Guo, Kai Xu, Qingqin Gao, Tianda Li, Jing Li, Qi Zhou, Wei Li
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-016-1014-9

UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing
Cited by: 3
Author(s): Daniel J. Park, Roger Li, Edmund Lau, Peter Georgeson, Tu Nguyen‐Dumont, Bernard J. Pope
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2019.00272

A QTL for Number of Teats Shows Breed Specific Effects on Number of Vertebrae in Pigs: Bridging the Gap Between Molecular and Quantitative Genetics
Cited by: 25
Author(s): Maren van Son, Marcos S. Lopes, Henry J Martell, Martijn F.L. Derks, Lars Erik Gangsei, Jørgen Kongsro, Mark N. Wass, Eli Grindflek, B. Harlizius
Software Mentions: 1
Published: over 5 years ago

10.3390/genes11121429

The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida
Cited by: 7
Author(s): Kyriakos Varypatakis, Pierre-Yves Véronneau, Peter Thorpe, Peter J. A. Cock, Joanne Tze-Yin Lim, Miles Armstrong, Sławomir Janakowski, Mirosław Sobczak, Ingo Hein, Benjamin Mimee, John T. Jones, Vivian C. Blok
Software Mentions: 1
Published: almost 4 years ago

10.1093/gbe/evaa044

A Study of Faster-Z Evolution in the Great Tit (Parus major)
Cited by: 10
Author(s): Kai Hayes, Henry J Barton, Kai Zeng
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-82050-5

Abundancy of polymorphic CGG repeats in the human genome suggest a broad involvement in neurological disease
Cited by: 21
Author(s): Dale John Annear, Geert Vandeweyer, Ellen Elinck, Alba Sanchis‐Juan, Courtney French, Lucy Raymond, R. Frank Kooy
Software Mentions: 1
Published: almost 4 years ago