| Tool | Use | Link |
|---|---|---|
| Chip enrich | Functional enrichment of ChIP enriched regions | http://chip-enrich.med.umich.edu/chipMain.jsp |
| REDItools | RNA editing detection | https://www.ncbi.nlm.nih.gov/pubmed/23742983 |
| Screw | Single-cell epigenomics workflow | https://github.com/Epigenomics-Screw/Screw |
| Google classroom | Handy teaching tool | https://classroom.google.com/h |
| Piazza QA platform | Free Q&A platform | https://piazza.com/ |
| Latex slides | Easy to edit slides (best for teaching) | https://www.overleaf.com/gallery/tagged/presentation#.WXMl9tOGP6Y |
| Moodle | Create your own course | https://moodle.org/?lang=nn |
| MultiQC | NGS data QC tool | http://multiqc.info/ |
| GraphSpace | Interactive graph sharing | http://graphspace.org/ |
| Common WL editor | Editor for CWL pipelines | https://github.com/rabix/composer |
| Coda | Denoising algorithm for ChIP-seq | https://github.com/kundajelab/coda |
| TargetFinder | Predicts Enhancer-promoter interactions | https://github.com/shwhalen/targetfinder |
| PEP | Predicts Enhancer-promoter interactions | |
| Dockstore | Cancer genomics workflows | https://dockstore.org/ |
| Well duplicates | Illumina index jumping detection | https://github.com/EdinburghGenomics/well_duplicates or https://sequencing.qcfail.com/articles/illumina-patterned-flow-cells-generate-duplicated-sequences/ |
| scRNA-seq analysis | scRNA-seq analysis Tutorial | https://htmlpreview.github.io/?https://github.com/ssarda/scRNAseq-workflow/blob/master/single_cell_analysis_workflow/Single%20Cell%20Analysis.html |
| PreTIS | Predicts 5' UTR TSS | http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005170 |
| WRENT | - | https://www.nature.com/articles/ncomms11663 |
| BIQ analyser | Tool for DNA methylation analysis | http://biq-analyzer.bioinf.mpi-inf.mpg.de/ |
| Epigraph | Tools for advanced epigenome analysis | http://epigraph.mpi-inf.mpg.de/WebGRAPH/ |
| netSurgeon | Move cells from one phenotypic stage to other | http://mblab.wustl.edu/software.html |
| OmicsDI | - | http://www.omicsdi.org/home |
| WDL pipelines | Framework for building NGS pipelines | https://software.broadinstitute.org/wdl/documentation/ |
| Neuroexpresso | Gene expression in Brain cell-types | https://github.com/oganm/neuroexpresso |
| SCREEN | Access ENCODE data along with some analysis features | http://screen.umassmed.edu/ |
| Labrador | A web based tool to manage and automate the processing of publicly available datasets | https://github.com/ewels/Labrador |
| Research parasite | Interesting one | http://researchparasite.com/ |
| Brabraham tools | Many NGS related tools | http://www.bioinformatics.babraham.ac.uk/projects/index.html |
| TITER | TSS detector by deep learning | https://github.com/zhangsaithu/titer |
| scanPy | Single cell analysis in python | https://github.com/theislab/scanpy |
| NetRepo | Fast permutation procedure for testing network module replication | https://github.com/InouyeLab/NetRep |
| GSoC | Google summer of code | https://github.com/obf/GSoC |
| AgreementMakerLight | Semantic Ontology Matching using External Resources | https://github.com/AgreementMakerLight |
| BioContainers/Mulled | Automatized Containerized Software Repository | https://github.com/BioContainers/mulled |
| salmon | fast transcript-level quantification from RNA-seq | https://github.com/COMBINE-lab/salmon/tree/factorizations |
| RNANR | software for determining secondary structures within RNA and their non-redundant sampling | https://github.com/JurMich/RNANR |
| Open science workshop | Science needs Open Source code - culture shift innovation workshop | MozillaFoundation/mozfest-program-2017#71 |
| Open Bioinformatics Foundation Travel Fellowships | Open Bioinformatics Foundation Travel Fellowships | https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md |
| f-scLVM | factorial single-cell latent variable model | https://github.com/PMBio/f-scLVM |
| scLVM | modelling framework for single-cell RNA-seq data | https://github.com/PMBio/scLVM |
| YAMP | Yet Another Metagenomic Pipeline | https://github.com/alesssia/YAMP |
| spector | R-package to analyse and quantify aberrations in DNA-sequencing data | https://github.com/anasrana/spector |
| Beer_ITS_analysis | BeerDeCoded first results using ITS | https://github.com/beerdecoded/Beer_ITS_analysis |
| ontology-tutorial | Ontology Tutorial at ISMB 2017 | https://github.com/bio-ontology-research-group/ontology-tutorial |
| ToolDog | Generating tool descriptors from bio.tools | https://github.com/bio-tools/ToolDog |
| bioinformatics.ca | Useful Bioinformatics resource | https://github.com/bioinformaticsdotca |
| biothings.api | Making high-performance API for biological annotation data | https://github.com/biothings/biothings.api |
| biothings_explorer | Python Package to explore the relationship between different biological entities using different databases | https://github.com/biothings/biothings_explorer |
| GATK | Genome Analysis ToolKit | https://github.com/broadinstitute/gatk |
| deepcpg | Deep neural networks for predicting CpG methylation | https://github.com/cangermueller/deepcpg |
| netics | network-based integration of multi-omics data for prioritizing cancer genes | https://github.com/cbg-ethz/netics |
| bcbio-nextgen | Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis | https://github.com/chapmanb/bcbio-nextgen |
| cwlviewer | A web application to view and share Common Workflow Language workflows | https://github.com/common-workflow-language/cwlviewer |
| SESAME | SESAME data mining application | https://github.com/csalexandre/SESAME |
| dockstore | VM/Docker sharing infrastructure and management component | https://github.com/ga4gh/dockstore |
| tool-registry-schemas | APIs for discovering genomics tools, their metadata and their containers | https://github.com/ga4gh/tool-registry-schemas |
| GALAXY training material | A collection of Galaxy-related training material | https://github.com/galaxyproject/training-material |
| 3D genome processing tutorial | A 3D genome data processing tutorial for ISMB/ECCB 2017 | https://github.com/hms-dbmi/3d-genome-processing-tutorial |
| GWASdb | Machine-curated database of genetic disease and genome-wide association studies | https://github.com/kuleshov/gwasdb/ |
| SPONGE | Sparse Partial correlation ON Gene Expression - an R package for fast and robust ceRNA network inference | https://github.com/mlist/SPONGE |
| nextflow-io | - | https://github.com/nextflow-io |
| ROBOT | Tool for working with Open Biomedical Ontologies | https://github.com/ontodev/robot |
| Rabix composer | Reproducible Analyses for Bioinformatics | https://github.com/rabix/composer/wiki/Introduction-to-Rabix-and-Rabix-Composer |
| PASTRI | Algorithm to infer tumor phylogenies from one or more bulk DNA sequencing samples | https://github.com/raphael-group/pastri |
| DeepBound | Predict the boundary of transcript start and end from RNA-seq reads alignment | https://github.com/realbigws/DeepBound |
| zeroSum | R-package for elastic net regularized regression with zero sum constraint | https://github.com/rehbergT/zeroSum |
| miniMDS | Inferring and plotting 3D structures from normalized Hi-C data | https://github.com/seqcode/miniMDS |
| bioentities | Resources for grounding biological entities from text and describing their hierarchical relationships. | https://github.com/sorgerlab/bioentities |
| SUSHI | Supporting User for SHell script Integration | https://github.com/uzh/sushi |
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Tools collected from different talks at ISMBECCB 2017
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