Paired Tag, MACSima, DNA Methylation requirement fix, script clean & update

.gitignore

@@ -5,5 +5,4 @@ node_modules
 /.vscode/*
 .directory
 # scripts
-scripts/*
 docs/metaTemplate/.gitignore

docs/assays/metadata/index.md

@@ -15,7 +15,7 @@ A list of available dataset types (data types from multiple supported assays), w
 | [CosMx Proteomics](https://hubmapconsortium.github.io/ingest-validation-tools/cosmx-proteomics/current/) [<img src="info3.png" width="14">](cosmx-proteomics "Attribute description")| CosMx Proteomics is a technology that enables the high-resolution, spatial analysis of proteins within their native tissue environment. It is part of the CosMx Spatial Molecular Imager (SMI) platform, which provides single-cell and subcellular resolution to map protein expression, cell states, and cell-cell interactions in FFPE and fresh frozen tissue samples. |
 | CosMx Transcriptomics [<img src="info3.png" width="14">](cosmx-transcriptomics "Attribute description")| Dataset generated from performing the CosMx Transcriptomics assay. |
 | [DESI](https://pmc.ncbi.nlm.nih.gov/articles/PMC6053038/) [<img src="info3.png" width="14">](DESI "Attribute description")| Desorption Electrospray Ionization (DESI), an ambient ionization technique that can be coupled to mass spectrometry (MS) for chemical analysis of samples at atmospheric conditions. Link to [DESI directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/desi/current/). |
-| DNA-Methylation [<img src="info3.png" width="14">](dna-methylation "Attribute description") | DNA methylation is a critical, reversible epigenetic mechanism in biomedical research involving the addition of a methyl group to DNA (usually cytosine in CpG islands), altering gene expression without changing the underlying sequence.  |
+| [DNA Methylation](https://hubmapconsortium.github.io/ingest-validation-tools/dna-methylation/current/) [<img src="info3.png" width="14">](dna-methylation "Attribute description") | DNA methylation is a critical, reversible epigenetic mechanism in biomedical research involving the addition of a methyl group to DNA (usually cytosine in CpG islands), altering gene expression without changing the underlying sequence. |
 | [Enhanced SRS](https://www.nature.com/articles/s41467-019-13230-1) [<img src="info3.png" width="14">](enhancedsrs "Attribute description")| Refers to improvements made to Stimulated Raman Scattering (SRS), a technique used in microscopy and spectroscopy for chemical imaging and analysis. These enhancements aim to improve sensitivity, spatial resolution, and other capabilities of SRS. Link to [Enhanced SRS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/enhanced-srs/current/). |
 | [GeoMx](https://nanostring.com/products/geomx-digital-spatial-profiler/spatial-multiomics-enabled-with-geomx-dsp/) [<img src="info3.png" width="14">](geomx "Attribute description")| A platform for spatial biology that analyzes RNA and protein expression within tissue sections which allows for non-destructive, in situ profiling of gene expression and protein levels from specific regions of interest (ROIs) within a tissue. Link to [GeoMx directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/geomx-ngs/current/). |
 | [HiFi](https://www.researchgate.net/publication/370676672_HiFi-Slide_spatial_RNA-Sequencing_v2) [<img src="info3.png" width="14">](hifi "Attribute description")| High-Fidelity Spatial Transcriptomic Slide (HiFi-Slide) sequencing, a super-resolution spatial transcriptomics sequencing technology, captures and spatially resolves genome-wide RNA expression in a submicron resolution for fresh-frozen tissue. Link to [HiFi directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/hifi-slide/current/). |
@@ -25,11 +25,13 @@ A list of available dataset types (data types from multiple supported assays), w
 | [IMC](https://docs.hubmapconsortium.org/assays/imc) [<img src="info3.png" width="14">](imc "Attribute description")| Combines standard immunohistochemistry with CyTOF mass cytometry to resolve the cellular localization of up to 40 proteins in a tissue sample. Link to [IMC directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/imc-2d/current/). |
 | [LC-MS](https://docs.hubmapconsortium.org/assays/lcms) [<img src="info3.png" width="14">](LC-MS "Attribute description")| Coupling of liquid chromatography (LC) to mass spectrometry (MS). Link to [LC-MS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/lcms/current/). |
 | [Light Sheet](https://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy) [<img src="info3.png" width="14">](Light-Sheet "Attribute description")| A fluorescence imaging technique that uses a thin sheet of laser light to illuminate a sample, allowing for high-resolution, 3D imaging with reduced photobleaching and phototoxicity; particularly useful for imaging large, thick, or delicate biological samples, like developing embryos or organoids. Link to [Light Sheet directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/lightsheet/current/). |
+| [MACSima](https://hubmapconsortium.github.io/ingest-validation-tools/macsima/current/) [<img src="info3.png" width="14">](macsima "Attribute description") | MACSima is a fully automated, high-content spatial biology system designed for ultra-high-plex, cyclic immunofluorescence imaging. It enables researchers to map hundreds of protein markers, and some RNAs, on a single tissue sample using [MICS technology (MACSima Imaging Cyclic Staining)](https://www.nature.com/articles/s41598-022-05841-4), combining deep phenotyping with spatial context. |
 | [MALDI-IMS](https://docs.hubmapconsortium.org/assays/maldi-ims) [<img src="info3.png" width="14">](MALDI "Attribute description") | Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) combines the sensitivity and molecular specificity of MS with the spatial fidelity of classical microscopy. Link to [MALDI-IMS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/maldi/current/). |
 | [MIBI](https://www.researchgate.net/figure/Multiplexed-ion-beam-imaging-workflow-for-high-resolution-spatial-proteomics-Here_fig1_349770840) [<img src="info3.png" width="14">](MIBI "Attribute description") | Preserved tissue sections, mounted on conductive substrates are incubated with unique isotopic transition metal-tagged antibody reporters. An oxygen primary ion beam rasters the sample surface, ejecting and ionizing the isotope reporters. Their masses are subsequently measured via a mass analyzer. Link to [MIBI directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/mibi/current/). |
 | [MERFISH](https://pubmed.ncbi.nlm.nih.gov/27241748/) [<img src="info3.png" width="14">](merfish "Attribute description") | A spatial transcriptomics technology that allows for the simultaneous imaging of hundreds to thousands of RNA species within single cells, providing both copy number and spatial distribution information. Link to [MERFISH directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/merfish/current/). |
 | [MUSIC](https://www.nature.com/articles/s41586-024-07239-w) [<img src="info3.png" width="14">](MUSIC "Attribute description") | A sequencing assay that allows profiling of gene expression, co-complexed DNA sequences, and RNA-chromatin interactions from the same single-cell nucleus. Both RNA and fragmented DNA within a nucleus are labelled with a unique cell barcode, enabling identification and matching of RNA and DNA sequences. Link to [MUSIC directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/music/current/). |
 | [MxIF](https://pmc.ncbi.nlm.nih.gov/articles/PMC9959383/#) [<img src="info3.png" width="14">](thicksectionmultiphotonmxif "Attribute description") | One version of MXIF (multiplexed fluorescence microscopy), an imaging platform whereby a large number of cellular and histological markers can be investigated on a single tissue section. Link to [TSM MxIF directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/thick-section-multiphoton-mxif/current/).|
+| [Paired Tag](https://hubmapconsortium.github.io/ingest-validation-tools/paired-tag/current/) [<img src="info3.png" width="14">](paired-tag "Attribute description") | Paired-Tag (parallel analysis of individual cells for RNA expression and DNA from targeted tagmentation by sequencing) is a high-throughput, single-cell multiomics method that simultaneously maps histone modifications and gene expression (transcriptome) in the same single cell. |
 | Pixel-seqV2 [<img src="info3.png" width="14">](pixel-seqv2 "Attribute description") | Pixel-seqV2 is a spatial transcriptomics method that utilizes polony gels to capture and sequence RNA, proteins or other molecules in tissues with high resolution. These polony gels are arrays of micron-scale DNA clusters, each containing a unique barcode, allowing for the mapping of molecules within their original spatial context in a tissue, thereby allowing researchers to study the spatial organization of cells and their gene expression profiles within tissues.|
 | [RNAseq](https://docs.hubmapconsortium.org/assays/rnaseq) [<img src="info3.png" width="14">](RNAseq "Attribute description") | While bulk RNAseq elucidates the average gene expression profile in cells comprising a tissue sample, single-cell RNAseq employs per-cell and per-molecule barcoding to enable single-cell resolution of the gene expression profile. Link to [RNAseq directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq/current/).|
 | [RNAseq with Probes](https://pmc.ncbi.nlm.nih.gov/articles/PMC5717752/#) [<img src="info3.png" width="14">](RNAseq-(with-probes) "Attribute description") | Uses probes to capture and enrich specific regions of the RNA for targeted sequencing, allowing for in-depth analysis of those regions. Link to [RNAseq with Probes directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq-with-probes/current/).|