Local Software repository

[Marcela]

Here you can find tools that have been created by local researchers

Please include a link to the tool, the author's name and a short description of what the tool does (as minimum)

[Leif Väremo]

Starting off the tools list by advertising two of the tools I have been part of developing:

Name: piano

Language: R

Link: www.sysbio.se/piano

Publication: https://doi.org/10.1093/nar/gkt111

Description: An R/Bioconductor package for gene-set analysis

Name: Kiwi

Language: Python

Link: www.sysbio.se/kiwi

Publication: https://doi.org/10.1186/s12859-014-0408-9

Description: Kiwi combines gene-set analyses with biological networks to visualize the interactions between gene-sets that are significant in a given biological system.

/Leif

[Martin]

Thanks for getting this list going Leif!

Name: ANT
Language: Python
Publication: https://doi.org/10.1021/acssynbio.5b00018
Description: Software for generating and evaluating degenerate codons. Such codons are often used in site-specific mutagenic approaches in protein engineering.

Martin

[S Abrahamsson]

Tool: SUPERSMART

Language: Perl

Link: http://www.supersmart-project.org/

Publication: https://academic.oup.com/sysbio/article-abstract/doi/10.1093/sysbio/syw066/2418028/Towards-a-Self-Updating-Platform-for-Estimating

Description: Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa (SUPERSMART)

[S Abrahamsson]

Tool: SpeciesGeoCoder

Language: Python

Link: https://github.com/mtop/speciesgeocoder

Publication: https://academic.oup.com/sysbio/article/doi/10.1093/sysbio/syw064/2670075/SpeciesGeoCoder-Fast-Categorization-of-Species

Description: SpeciesGeoCoder is a free software package for coding species occurrences into user-defined units for e.g. biogeographic analyses.

[S Abrahamsson]

Tool: Qlucore Omics Explorer

Link: http://www.qlucore.com/

Publication: Dongfeng Chen, Junxiong Zheng, Natalija Gerasimcik, Kristina Lagerstedt, Helene Sjögren, Jonas Abrahamsson, Linda Fogelstrand, Inga-Lill Mårtensson. The Expression Pattern of the Pre-B Cell Receptor Components Correlates with Cellular Stage and Clinical Outcome in Acute Lymphoblastic Leukemia. PLOSOne, 2016

Yingyu Sun*, Wei zhang*, Dongfeng Chen*, Yuhong Lv*, Junxiong zheng, Henrik lilljebjörn, Liang Ran, Zhaoshi Bo, Charlotte Soneson, Hans Olov Sjogern, Leif G. Salford, Jianguang Ji, Pim J. French, Thoas Fioretos, Tao Jiang, and Xiaolong Fan. A glioma classification scheme based on coexpression modules of EGFR and PDGFRA. PNAS, 2014, 111(9): 3538-3543 (* Equal contribution to this work)  

  

Description: Because Qlucore Omics Explorer is so easy to use, you don't need to be an expert in analysis to use it. The current user base spans a broad range of professions, from bioinformaticians, biologists, statisticians and chemists to medical doctors, students and professors.

[S Abrahamsson]

Tool: Metaxa

Language: Perl

Link: http://microbiology.se/software/metaxa/

Publication: http://www.springerlink.com/content/n56h854713187159/

Description: A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

[S Abrahamsson]

Tool: Metaxa2

Language: Perl

Link: http://microbiology.se/software/metaxa2/

Publication: http://dx.doi.org/10.1111/1755-0998.12399

Description: A software tool for automated detection and classification of ribosomal rRNA sequences in metagenomes and environmental sequencing datasets

[S Abrahamsson]

Tool: ITSx

Language: Perl

Link: http://microbiology.se/software/itsx/

Publication: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12073/abstract

Description: A software for detection and extraction of the ITS1 and ITS2 barcoding regions from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing sets

[S Abrahamsson]

Tool: FARAO

Language: Perl

Link: http://microbiology.se/software/farao/

Publication: http://dx.doi.org/10.1093/bioinformatics/btw499

Description: The Flexible All-Round Annotation Organizer, a set of software tools that constitute as a highly configurable way to handle sequence annotation and coverage information.

[S Abrahamsson]

Tool: Megraft

Language: Perl

Link: http://microbiology.se/software/megraft/

Publication: http://www.sciencedirect.com/science/article/pii/S0923250812000964

Description: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.

[S Abrahamsson]

Tool: TriMetAss

Language: Perl

Link: http://microbiology.se/software/trimetass/

Publication: http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00648/abstract

Description: The Trinity-based Iterative Metagenomics Assembler

[S Abrahamsson]

Tool: PETKit

Language: Perl

Link: http://microbiology.se/software/petkit/

Publication: -

Description: A set of tools to ease the use of sequences from large-scale sequencing projects, generating paired-end reads.

[S Abrahamsson]

Tool: Atosh

Language: Perl

Link: http://iris.ut.ee/unite/temp/plutof2/clipboard_seq.php?action=analysis&program=ATOSH

Publication: http://onlinelibrary.wiley.com/doi/10.1111/mec.12481/abstract

Description: Assign to Species Hypothesis; this script underlies part of the UNITE database

[S Abrahamsson]

Tool: BacMet-Scan

Language: Perl

Link: http://bacmet.biomedicine.gu.se/download_temporary.html

Publication: http://nar.oxfordjournals.org/content/42/D1/D737.full

[S Abrahamsson]

Tool: MethPed: A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

Link: https://www.bioconductor.org/packages/release/bioc/html/MethPed.html

Publication: 

1. https://www.ncbi.nlm.nih.gov/pubmed/26157508

2. https://www.ncbi.nlm.nih.gov/pubmed/27370569

Description:

Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

[S Abrahamsson]

Tool:Scan-o-matic

Language: Python, JavaScript, HTML, CSS

Link: https://github.com/local-minimum/scanomatic/

Publication: http://g3journal.org/content/6/9/3003.full 

Description: High throughput and high accuracy microbial growth phenotyping platform

[S Abrahamsson]

Tool: HattCI

Language: C

Link: http://github.com/maribuon/HattCI

Publication: HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models. Pereira, Mariana Buongermino; Wallroth, Mikael; Kristiansson, Erik; and Axelson-Fisk; Marina. Journal of Computational Biology. November 2016, 23(11): 891-902. doi:10.1089/cmb.2016.0024.

Description: HattCI is a generalized hidden Markov model implemented in C to predict attC sites, the recombination site present in gene cassettes mobilized by integrons. HattCI was developed to fast handle large datasets, such as assembled metagenomic data.