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Adding an additional tag as per #25.
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Added a couple new items indicated in that discussion as well.
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zackbatist committed Jul 23, 2021
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10 changes: 6 additions & 4 deletions open-archaeo.csv
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Expand Up @@ -360,8 +360,8 @@ schmutzi,Maximum a posteriori estimate of contamination for ancient samples.,htt
Sex.DetERRmine,"Calculate the relative coverage of X and Y chromosomes, and their associated error bars, from the depth of coverage at specified SNPs.",https://github.com/TCLamnidis/Sex.DetERRmine,,,,,,,,,,,,,,TCLamnidis,,,,,Scripts,Python,Archaeogenetics,Low-coverage adapted population-genetics tools,,,,,https://archive.org/details/github.com-TCLamnidis-Sex.DetERRmine_-_2020-06-11_18-13-25
MultiVCFAnalyzer,"A SNP filtering and SNP alignment generation tool, designed around (but not limited to) low coverage ancient DNA data.",https://github.com/alexherbig/MultiVCFAnalyzer,,,,,,,,,,,,,,alexherbig,,,,,Standalone software,,Archaeogenetics,Low-coverage adapted population-genetics tools,,,,,https://archive.org/details/github.com-alexherbig-MultiVCFAnalyzer_-_2020-06-10_11-52-02
PMDtools,Compute postmortem damage patterns and decontaminate ancient genomes.,https://github.com/pontussk/PMDtools,,,,,,,,,,,,,,pontussk,,,,,Standalone software,,Archaeogenetics,Low-coverage adapted population-genetics tools,,,,,https://archive.org/details/github.com-pontussk-PMDtools_-_2021-04-20_21-15-07
maximum-likelihood-relatedness-estimation,Infer biological relatedness from low coverage 2nd generation sequencing data.,https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation,,,,,,,,,,,https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/wiki,,,COMBINE-lab,,,,,Standalone software,,Archaeogenetics,Low-coverage adapted population-genetics tools,,,,,
READ,"A method to infer the degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for a pair of low-coverage individuals.",,,,https://bitbucket.org/tguenther/read/src/master/,,,,,,,,,,,tguenther,,,,,Standalone software,,Archaeogenetics,Low-coverage adapted population-genetics tools,,,,,
maximum-likelihood-relatedness-estimation,Infer biological relatedness from low coverage 2nd generation sequencing data.,https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation,,,,,,,,,,,https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/wiki,,,COMBINE-lab,,,,,Standalone software,,Archaeogenetics,Low-coverage adapted population-genetics tools,aDNA kinship,,,,
READ,"A method to infer the degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for a pair of low-coverage individuals.",,,,https://bitbucket.org/tguenther/read/src/master/,,,,,,,,,,,tguenther,,,,,Standalone software,,Archaeogenetics,Low-coverage adapted population-genetics tools,aDNA kinship,,,,
pileupcaller,Sample alleles from low coverage sequence data.,https://github.com/stschiff/sequenceTools,,,,,,,,,,,,,,stschiff,,,,,Standalone software,,Archaeogenetics,aDNA damage-aware genotypers,,,,,https://archive.org/details/github.com-stschiff-sequenceTools_-_2021-06-14_12-16-40
angsd,Program for analysing next generation sequencing data.,https://github.com/ANGSD/angsd,,,,,,,,,,,http://www.popgen.dk/angsd/index.php/ANGSD,,,ANGSD,,,,,Standalone software,,Archaeogenetics,Low-coverage contamination estimation,,,,,https://archive.org/details/github.com-ANGSD-angsd_-_2021-06-18_10-14-14
hapROH,Software to call ROH from ancient and present-day DNA using reference haplotypes.,https://github.com/hringbauer/hapROH,,,,,,,,,https://pypi.org/project/hapROH/,,,,,hringbauer,,,,,Packages and libraries,Python,Archaeogenetics,Low-coverage adapted population-genetics tools,,,,,https://archive.org/details/github.com-hringbauer-hapROH_-_2021-06-23_15-01-24
Expand Down Expand Up @@ -418,7 +418,7 @@ spDates,Analysis of spatial gradients in radiocarbon dates.,https://github.com/j
rxpand,Radiocarbon dates for the spread of farming and ceramics in tropical South America.,https://github.com/jgregoriods/rxpand,,,,,,,,,,,,,,jgregoriods,,,,,Lists and datasets,R,Datasets,"Radiocarbon dating, calibration and sequencing",,,,,https://archive.org/details/github.com-jgregoriods-rxpand_-_2021-06-16_08-05-37
katun,Tools for converting between Maya and Western calendars.,https://github.com/jgregoriods/katun,,,,,,,,,,,https://jgregoriods.github.io/katun/,,,jgregoriods,,,,,Standalone software,,Chronological modelling,,,,,,https://archive.org/details/github.com-jgregoriods-katun_-_2021-05-27_03-02-18
maya-calendar,Tools for converting between Maya and Western calendars.,https://github.com/jgregoriods/maya-calendar,,,,,,,,,,,https://jgregoriods.github.io/maya-calendar/dist/,,,jgregoriods,,,,,Standalone software,,Chronological modelling,,,,,,https://archive.org/details/github.com-jgregoriods-maya-calendar_-_2021-05-27_02-40-14
tkgwv2,An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data.,https://github.com/danimfernandes/tkgwv2,,,,,,,,,,,,,,danimfernandes,,,,,Standalone software,,Archaeogenetics,,,,,,https://archive.org/details/github.com-danimfernandes-tkgwv2_-_2021-07-02_09-41-04
tkgwv2,An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data.,https://github.com/danimfernandes/tkgwv2,,,,,,,,,,,,,,danimfernandes,,,,,Standalone software,,Archaeogenetics,aDNA kinship,,,,,https://archive.org/details/github.com-danimfernandes-tkgwv2_-_2021-07-02_09-41-04
chronochrt,Building chronological charts easily with R.,,,https://gitlab.com/roset/chronochrt,,,,,,,,,,,,roset,,,,,Packages and libraries,R,Chronological modelling,,,,,,
Image enhancement process tool,This software implements five state of the art algorithms aimed to enhance the quality of underwater images.,,,,,,,,,,,,https://imareculture.eu/downloads/project-tools/image-enhancement-process-tool/,,,iMare Culture,,,,,Standalone software,,Underwater archaeology,Photography,,,,,
3D libraries of ships,A 3D library of ancient (classical era) ships.,,,,,,,,,,,,https://imareculture.eu/downloads/project-tools/3d-libraries-of-ships/,,,iMare Culture,,,,,Lists and datasets,,3D modelling,Datasets,,,,,
Expand All @@ -430,4 +430,6 @@ List of Resources for getting started with (teaching) digital methods,A short li
ABC of Archaeobotanical Open Science,A list of terms related to open archaeobotanical science.,,,,,,,,https://ekaroune.github.io/The-Open-Archaeobotanist/abcofarchaeobotanicalopenscience/,,,,,,,ekaroune,,,,,Lists and datasets,,Lists,Educational resources and practical guides,,,,,
Open-Science-in-Phytolith-Research,"Project to create community awareness of open science practices, provide training and establish a working group for open science.",https://github.com/EKaroune/Open-Science-in-Phytolith-Research,,,,,,,,,,,https://ekaroune.github.io/Open-Science-in-Phytolith-Research/,,,ekaroune,,,,,Guides,,Educational resources and practical guides,,,,,,
IsoArcH,Open access and collaborative isotope database for bioarcheological samples.,,,,,,https://twitter.com/isoarch_eu,,,,,,https://isoarch.eu/,,,IsoArcH,,,,,Lists and datasets,,Datasets,,,,,,
Bridging the Gap ENCODE Database,Shared definitions of digital competences needed by graduate students in the programmes focusing on written cultural heritage.,,,,,,,,,,,,https://encode.uni-hamburg.de/index.html,,,Bridging the Gap ENCODE Database,,,,,"Specifications, protocols and schemas",,Schemas and ontologies,Educational resources and practical guides,Ethics and professional development,,,,
Bridging the Gap ENCODE Database,Shared definitions of digital competences needed by graduate students in the programmes focusing on written cultural heritage.,,,,,,,,,,,,https://encode.uni-hamburg.de/index.html,,,Bridging the Gap ENCODE Database,,,,,"Specifications, protocols and schemas",,Schemas and ontologies,Educational resources and practical guides,Ethics and professional development,,,,
grups,A collection of Python and R scripts that can be used to simulate the pairwise genetic distances between human individuals in a provided test pedigree.,https://github.com/sameoldmike/grups/,,,,,,,,,,,,,,sameoldmike,,,,,Scripts,,Archaeogenetics,aDNA kinship,,,,,
NgsRelate,"Infer relatedness, inbreeding coefficients and many other summary statistics for pairs of individuals.",https://github.com/ANGSD/NgsRelate,,,,,,,,,,,,,,ANGSD,,,,,Standalone software,,Archaeogenetics,aDNA kinship,,,,,
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