| 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 |
Last active
January 19, 2019 02:13
-
-
Save itsvenu/89b812001ddd60425d856b54550ec35c to your computer and use it in GitHub Desktop.
Tools collected from different talks at ISMBECCB 2017
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment