Tools with dead links (404, timeout, connection refused, etc.).

Data Sets

• Hartwig WGS (requires data request): https://www.hartwigmedicalfoundation.nl/en/wgs-database/

  • Status: HTTP 404: HTTP Error 404: Not Found

• Cloud resource for filtering 1kg data

  • http://bamsi.research.it.uu.se/
  • Python API: https://github.com/NGDSG/BAMSI-API
  • Status: HTTP 503: HTTP Error 503: Service Unavailable

General Programming Resources

C/C++

• Succinct de Bruijn Graphs: http://alexbowe.com/succinct-debruijn-graphs/
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HPC

• Petuum: http://petuum.github.io/

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• Efficient tabular storage: http://matthewrocklin.com/blog/work/2015/08/28/Storage/

  • Status: HTTP 404: HTTP Error 404: Not Found

• Common runtime for various libraries (e.g. Pandas, TensorFlow) that speeds up execution when interfacing the libraries with each other: https://weld-project.github.io/

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

Other

• Aether manages bidding for AWS and Azure credits: http://aether.kosticlab.org/
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Python

• RStudio for python: https://www.yhat.com/products/rodeo

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• FFI

  • GO transplier: https://github.com/google/grumpy
  • Calling Rust libraries from python: https://medium.com/@caulagi/complementing-python-with-rust-657a8cb3d066#.6in8v0bte
  • pyjamas: javascript bridge
  • Status: Archived repo

• skbio: http://scikit-bio.org/docs/0.4.1/index.html

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R

• Applying tidy principals to GRanges: https://bioconductor.org/packages/release/bioc/html/plyranges
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Find packages

• http://www.computerworld.com/article/2497464/business-intelligence/business-intelligence-60-r-resources-to-improve-your-data-skills.html
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Misc

• Find root of current package: https://krlmlr.github.io/here/
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Reporting

• Nozzle: https://confluence.broadinstitute.org/display/GDAC/Nozzle
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Reproducibility/Containerization

• GUI frontend to IPython: http://nwhitehead.github.io/pineapple/

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• Stencila: interesting alternative to Jupyter notebooks and R markdown https://stenci.la/

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• Creating reproducible workflows with R Markdown documents: https://jdblischak.github.io/workflowr/

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Building Pipelines

• SnakeMake

  • SnakeChunks: components for SnakeMake https://github.com/SnakeChunks/SnakeChunks
  • Create command line programs from SnakeMake workflows: https://github.com/nh13/snakeparse
  • GUI: http://sequana.readthedocs.io/en/master/sequanix.html
  • Status: Last push 2408 days ago (2019-09-07), 3 open issues

• Toil: http://toil.readthedocs.io/en/latest/installation.html

  • Status: HTTP 404: HTTP Error 404: Not Found

• Generate data type-specific compression formats: http://algorithms.cnag.cat/cargo/

  • Status: HTTP 404: HTTP Error 404: Not Found

• Pipe output of a shell command to a website (unfortunately can't be used in NIH HPC since nodes do not allow network connections): https://seashells.io/

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Genomics

Candidate Prioritization

• SnpNexus: http://snp-nexus.org/IW-Scoring/
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Databases

• Super-Enhancer Archive: http://www.bio-bigdata.com/SEA/

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• GWAS database: http://jjwanglab.org/gwasdb

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• rVarBase: regulatory features of human genetic variants http://rv.psych.ac.cn/

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• BISQUE: convert between database identifiers http://bisque.yulab.org/

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• Database of disease-associated methylation: http://202.97.205.78/diseasemeth/

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• Human histone modifications: http://www.tongjidmb.com/human/index.html

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• iRegNet3D: SNP-focused catalog of TF-TF, TF-DNA, and DNA-DNA interactions http://iregnet3d.yulab.org/index/

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• Interactive multi-omics tissue assay database: https://ccb-web.cs.uni-saarland.de/imota/

  • Status: HTTP 503: HTTP Error 503: Service Unavailable

• Database of genetic variant effects on gene expression: https://xhaubem01.u.hpc.mssm.edu/gwas2genes/

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• PharmacoDB

  • Search multiple cancer pharmacogenomic databases with a single query
  • Software is GPL licensed; target databases have various licenses
  • http://pharmacodb.pmgenomics.ca
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• Database of druggable variant information (web only): http://depo-dinglab.ddns.net/

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• Search publications and clinical trials by genes/variants/drugs https://vist.informatik.hu-berlin.de/

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Functional Enrichment/Ontology

• Variant Set

  • VSE: https://cran.r-project.org/web/packages/VSE/vignettes/my-vignette.html
  • Functional enrichment with LD correction
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• MESH

  • MeSH over-representation: http://www.bioconductor.org/packages/release/bioc/vignettes/meshr/inst/doc/MeSH.pdf
  • meshes: https://guangchuangyu.github.io/meshes/
  • Status: HTTP 404: HTTP Error 404: Not Found

Motif/TFBS

• Circular logos: http://bioinformaticstools.mayo.edu/circularlogo/index.html
  • Status: HTTP 403: HTTP Error 403: Forbidden

Network Analysis

• PAXToolsR: http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html

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• ancGWAS: post GWAS association with protein-protein interaction networks http://www.cbio.uct.ac.za/~emile/software.html

  • Status: HTTP 404: HTTP Error 404: Not Found

Prediction

• Chromatin accessibility
  • SCM: http://scm.csail.mit.edu/
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Sequence Analysis

Chromatin Interactions

• Model 3D chromosome structure from Hi-C contact maps + optional FISH constraints: https://github.com/yjzhang/FISH_MDS.jl, https://github.com/yjzhang/3DC-Browser

  • Status: GitHub repo not found

• Predicting TADs from histone modifications: https://cb.utdallas.edu/CITD/index.htm#ajax=home

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Footprinting

• NucID: nucleosome positioning from DNase-seq https://jianlingzhong.github.io/NucID/
  • Status: HTTP 404: HTTP Error 404: Not Found

General-purpose

• k-mer hashing: https://github.com/czbiohub/kmer-hashing
  • Status: GitHub repo not found (404)

Methylation

• QC

  • ME-plot: Error detection and correction in bisulfite-converted sequencing reads https://github.com/joshuabhk/methylsuite
  • Correction for cell-type composition: http://www.cs.tau.ac.il/~heran/cozygene/software/refactor.html
  • Status: Last push 3835 days ago (2015-10-11), 1 open issues

• Simulation

  • Sherman: http://www.bioinformatics.babraham.ac.uk/projects/sherman/
  • DNemulator uses a similar idea for simulating cytosine metylation depending on CG context and bisulfite converstion rates: http://cbrc3.cbrc.jp/~martin/dnemulator/
  • WGBSsuite: includes a hierarchical HMM for read simulation: https://github.com/SystemsGeneticsSG/WGBSSuite/blob/master/simulate_WGBS.R
    • Ideas about additional parameters to add http://www.genetics.org/content/genetics/early/2017/02/16/genetics.116.195008.full.pdf
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Peak-based

ChIP-seq

• Motif assessment: http://www.bioinf.ict.ru.ac.za/

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• Web-based tool to compute enrichment at a variety of genomic features: http://liulab.dfci.harvard.edu/CEAS/

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• QC https://bioconductor.org/packages/devel/bioc/html/ChIC.html

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QC

• DOGMA: Measure completeness of a transcriptome or proteome assembly https://ebbgit.uni-muenster.de/domainWorld/DOGMA/

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• SamStat: http://samstat.sourceforge.net/

  • Status: HTTP 404: HTTP Error 404: Not Found

RNA

• Annotations

  • Reassembly and annotation of public data for multi-tissue transcriptome map: http://big.hanyang.ac.kr/CAFE
  • Annotates transcripts with intron retention so they can be ignored (reduces assembly bias): https://github.com/Shao-Group/irtool
  • Status: HTTP 502: HTTP Error 502: Proxy Error

• Search

  • BloomTree: http://www.cs.cmu.edu/∼ckingsf/software/bloomtree/
  • SBTs https://github.com/medvedevgroup/bloomtree-allsome
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Single-cell

• Optimized references: https://www.thepoolab.org/resources

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• Gene/Transcript counting

  • Modified version of Kallisto: https://github.com/govinda-kamath/clustering_on_transcript_compatibility_counts
  • DISCO: https://pbtech-vc.med.cornell.edu/git/mason-lab/disco/tree/master
  • ESAT: http://garberlab.umassmed.edu/software/esat/
  • Status: Last push 2700 days ago (2018-11-19), 0 open issues

Simulation

• Perturbation of genomic intervals http://bedshift.databio.org/en/latest/
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Variant annotation

• VCF visualization with Circos plot: http://legolas.ariel.ac.il/~tools/CircosVCF/

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• Protein sequence and structure annotation for variants https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/DisaStr/GetPage.pl?varmap=TRUE

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Pairwise alignment

Algorithms

Semi-global

http://www.bioinf.uni-freiburg.de/Lehre/Courses/2013_SS/V_Bioinformatik_1/lecture4.pdf) is global alignment with an optional gap at the end(s).

• Status: HTTP 404: HTTP Error 404: Not Found

Promising methods without software implementation

• ABBA http://abba.systems-genetics.net

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• MR_eQTL: https://github.com/PrincetonUniversity/MR_eQTL

  • Status: GitHub repo not found (404)

Publication/Archiving

CV

• Using RMarkdown: https://ropenscilabs.github.io/vitae/
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Code/Data sharing

• GitHub: https://github.com/blog/1986-announcing-git-large-file-storage-lfs

  • Status: GitHub repo not found

• OSF API: https://test-api.osf.io/v2/docs/

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• ThinkLab: https://thinklab.com/

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• QRI: https://qri.io/

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Writing

• Pandoc scholar: https://github.com/pandoc-scholar/pandoc-scholar

  • Nice paper showing example of generating manuscripts for two different journals: https://peerj.com/preprints/2648.pdf
  • Status: Last push 1170 days ago (2023-01-27), 9 open issues

• Editoria: https://editoria.pub/

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• Recommend papers to cite based on your bibliography: http://labs.semanticscholar.org/citeomatic/

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• Slideboards: Mashup of slides and FAQ to explain a publication http://slideboard.herokuapp.com/

  • Status: HTTP 404: HTTP Error 404: Not Found

Statistics/Machine Learning

Data Sets

• https://medium.com/@olivercameron/20-weird-wonderful-datasets-for-machine-learning-c70fc89b73d5#.9e5byk1mo
  • Status: HTTP 403: HTTP Error 403: Forbidden

Deep Learning

• Platforms
  • Aetros: http://aetros.com/
  • Status: HTTP 0: <urlopen error [Errno 61] Connection refused>

Methods/algorithms

• Fast exact calculation of p-values in Friedman rank sum test: http://www.ru.nl/publish/pages/726696/friedmanrsd.zip

  • The Friedman test is for testing whether any columns are consistently different from other columns in a matrix
  • Status: HTTP 404: HTTP Error 404: Not Found

• Forecasting from time-series data: https://facebookincubator.github.io/prophet/ (this is a retail-centric model from Facebook, but could be adapted to biological data)

  • Status: HTTP 404: HTTP Error 404: Not Found

Python

• Tools for data mining, NLP, ML, network analysis: http://www.clips.ua.ac.be/pages/pattern

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• scikit-learn-compatible package for graph statistics: https://graspy.neurodata.io/

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Web APIs

• Google Prediction: https://cloud.google.com/prediction
  • Status: HTTP 404: HTTP Error 404: Not Found

Visualization

Javascript

• http://blog.webkid.io/javascript-chart-libraries/

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• D3.js: https://pub.beakernotebook.com/#/publications/560c9f9b-14e6-4d95-8e78-cc0a60bf4e5a?fullscreen=false

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• Circos for Javascript: http://bioinfo.ibp.ac.cn/biocircos/

  • Status: HTTP 0: Remote end closed connection without response

• Dataviz components built on top of D3: http://nivo.rocks/?ref=producthunt#/components

  • Status: HTTP 402: HTTP Error 402: Payment Required

• Muze: https://www.charts.com/muze

  • Status: HTTP 0: <urlopen error [Errno 61] Connection refused>

R

Data Types

• Network visualization from R using vis.js: http://dataknowledge.github.io/visNetwork/
  • Status: HTTP 404: HTTP Error 404: Not Found

ggplot2

• Gallery of extensions: http://www.ggplot2-exts.org/gallery/

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• Color palattes

  • Color scales with clustering (would want to adapt this to ggplot): https://github.com/schne
  • ggSci: https://ggsci.net/
  • Status: HTTP 404: HTTP Error 404: Not Found

• ggrepel: displaying text labels with minimal overlapping https://github.com/slowkow/ggrepelrd/d3-scale-cluster

  • Status: GitHub repo not found (404)

• Beeswarm: https://github.com/eclarke/ggbeeswarm: plot overlapping points without jitter

  • Status: GitHub repo not found

• Breve is a mac application that displays large tables in a way that makes it easy to identify patterns and missing data http://breve.designhumanities.org/

  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>

• Making colorblind-friendly figures: http://bconnelly.net/2013/10/creating-colorblind-friendly-figures/

  • Status: HTTP 404: HTTP Error 404: Not Found

• Feedback: http://helpmeviz.com/

  • Status: HTTP 503: HTTP Error 503: Service Unavailable

• Circos-like visualization of chromosome structure with support for multiple data types https://rondo.ws

  • Status: HTTP 0: <urlopen error [Errno 61] Connection refused>

• VCF

  • CircosVCF
    • Visualization of variant calls from a VCF on a CIRCOS plot
    • CircosVCF: http://legolas.ariel.ac.il/~tools/CircosVCF
  • https://github.com/compbiocore/VariantVisualization.jl
  • Status: HTTP 0: <urlopen error [Errno 8] nodename nor servname provided, or not known>