Download JAR files tagged by gene with all dependencies

gene-name-mapping-resource-creation from group de.julielab (version 1.0.1)

This project assembles code and files required to build the dictionaries and indexes used by the Gene Mapper.

Group: de.julielab Artifact: gene-name-mapping-resource-creation
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Artifact gene-name-mapping-resource-creation
Group de.julielab
Version 1.0.1
Last update 19. October 2020
Organization not specified
URL Not specified
License not specified
Dependencies amount 10
Dependencies slf4j-api, jcore-types, piccolo, logback-classic, julie-xml-tools, costosys, gene-name-mapping-ae, julielab-java-utilities, jcore-descriptor-creator, assertj-core,
There are maybe transitive dependencies!

jcore-feature-value-replacement-ae from group de.julielab (version 2.6.1)

This analysis engine simply replaces feature values of feature structures with other values as defined by an external resource, e.g. file. For instance, all NCBI Gene IDs could be mapped to Ensemble IDs.

Group: de.julielab Artifact: jcore-feature-value-replacement-ae
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Artifact jcore-feature-value-replacement-ae
Group de.julielab
Version 2.6.1
Last update 18. December 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-feature-value-replacement-ae
License BSD-2-Clause
Dependencies amount 3
Dependencies jcore-utilities, jcore-descriptor-creator, junit-jupiter-engine,
There are maybe transitive dependencies!

jcore-bionlpgold-pred-gene-merge-ae from group de.julielab (version 2.6.0)

Given the gold BioNLP ST gene mentions and other gene mentions - possibly from gene recognizer - merges the two different sources of genes. For simplicity, this component employs two different types to represent genes. The BioNLP ST reader uses the de.julielab.jcore.types.Gene type. The other genes should be realized with de.julielab.jcore.types.Protein annotations.

Group: de.julielab Artifact: jcore-bionlpgold-pred-gene-merge-ae
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Artifact jcore-bionlpgold-pred-gene-merge-ae
Group de.julielab
Version 2.6.0
Last update 25. November 2022
Organization JULIE Lab Jena, Germany
URL https://github.com/JULIELab/jcore-base/tree/master/jcore-bionlpgold-pred-gene-merge-ae
License BSD 2-Clause
Dependencies amount 5
Dependencies jcore-utilities, slf4j-api, jcore-types, jcore-descriptor-creator, junit-jupiter-engine,
There are maybe transitive dependencies!

pepgenome from group io.github.bigbio (version 1.1.1)

PepGenome uses transcript translations and reference gene annotations to identify the genomic loci of peptides and post-translational modifications. Multiple occurrences of peptides in the input data resulting in the same genomic loci will be collapsed as a single occurrence in the output.

Group: io.github.bigbio Artifact: pepgenome
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Artifact pepgenome
Group io.github.bigbio
Version 1.1.1
Last update 18. August 2021
Organization Big Bioinformatics Open Stack
URL https://github.com/bigbio/pepgenome/
License Apache 2.0
Dependencies amount 9
Dependencies jmzidentml, pgatk-io, pia, commons-cli, commons-lang3, lombok, sizeof, mapdb, log4j,
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dragontool from group de.julielab (version 1.3.3)

Copy of the dragontools from http://dragon.ischool.drexel.edu with very limited functionality due to the lack of publicly available Maven dependencies. Used in JULIELab JCoRe as dependency for the BANNER gene tagger.

Group: de.julielab Artifact: dragontool
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1 downloads

Artifact dragontool
Group de.julielab
Version 1.3.3
Last update 10. August 2018
Organization not specified
URL Not specified
License not specified
Dependencies amount 3
Dependencies gate-core, jwnl, commons-httpclient,
There are maybe transitive dependencies!

jcore-mutationfinder-ae from group de.julielab (version 2.6.1)

An analysis engine to recognize mentions of gene point mutations in document text. This is a wrapper around the original MutationFinder (http://mutationfinder.sourceforge.net/), published in the following paper: MutationFinder: A high-performance system for extracting point mutation mentions from text J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter; Bioinformatics, 2007 23(14):1862-1865; doi:10.1093/bioinformatics/btm235;

Group: de.julielab Artifact: jcore-mutationfinder-ae
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Artifact jcore-mutationfinder-ae
Group de.julielab
Version 2.6.1
Last update 18. December 2022
Organization not specified
URL Not specified
License BSD-2-Clause
Dependencies amount 6
Dependencies oro, junit-jupiter-engine, jcore-types, jcore-descriptor-creator, slf4j-api, assertj-core,
There are maybe transitive dependencies!

SVMAttributeEval from group nz.ac.waikato.cms.weka (version 1.0.2)

Evaluates the worth of an attribute by using an SVM classifier. Attributes are ranked by the square of the weight assigned by the SVM. Attribute selection for multiclass problems is handled by ranking attributes for each class seperately using a one-vs-all method and then "dealing" from the top of each pile to give a final ranking. For more information see: I. Guyon, J. Weston, S. Barnhill, V. Vapnik (2002). Gene selection for cancer classification using support vector machines. Machine Learning. 46:389-422.

Group: nz.ac.waikato.cms.weka Artifact: SVMAttributeEval
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Artifact SVMAttributeEval
Group nz.ac.waikato.cms.weka
Version 1.0.2
Last update 26. April 2012
Organization University of Waikato, Hamilton, NZ
URL http://weka.sourceforge.net/doc.packages/SVMAttributeEval
License GNU General Public License 3
Dependencies amount 1
Dependencies weka-dev,
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gene-mapper-experimental-base from group de.julielab (version 1.0.0)

This project has a lot of business classes to work with genes and related named entities. Genes are part of a GeneDocument and may have gold IDs as well as mapped/predicted IDs. Another large part are species because most (all?) gene ID databases are species specific. So there are also classes or members to represent species mentions and the assignment of species IDs (taxonomy IDs) to genes. There is little to no business logic herein. This project is only useful as building block in other projects dealing with species assignment, gene ID mapping or similar efforts.

Group: de.julielab Artifact: gene-mapper-experimental-base
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Artifact gene-mapper-experimental-base
Group de.julielab
Version 1.0.0
Last update 03. December 2022
Organization JULIE Lab Jena, Germany
URL Not specified
License BSD-2-Clause
Dependencies amount 21
Dependencies commons-lang3, commons-text, julielab-java-utilities, slf4j-api, lucene-analyzers-common, guava, julielab-ranklib-mallet, jcore-mallet-2.0.9, libsvm, spark-core, guice, julie-xml-tools, julielab-entity-evaluator, ehcache, cache-api, annotations, commons-codec, commons-io, junit-jupiter-engine, assertj-core, com.wcohen.secondstring,
There are maybe transitive dependencies!

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