From 2485b47ad5b90820a73e5377c9862bc3e573f8ac Mon Sep 17 00:00:00 2001 From: Viktoria Petrova <vipet103@hhu.de> Date: Wed, 22 Jan 2025 11:27:44 +0100 Subject: [PATCH] add tables to READMEs --- ...d enhancer regions _ Oxford Academic.html" | 3 -- .../643701de45aa460012e1032e.js.download" | 3 -- .../Site.css" | 3 -- .../css" | 3 -- .../f.txt" | 3 -- .../global.css" | 3 -- .../gtm.js.download" | 3 -- .../icons.css" | 3 -- .../jquery-migrate-1.4.1.min.js.download" | 3 -- .../jquery.min.js.download" | 3 -- .../ntpagetag.js.download" | 3 -- .../ps.js.download" | 3 -- .../saved_resource(1).html" | 3 -- .../saved_resource(2).html" | 3 -- .../saved_resource.html" | 3 -- .../scm.proxylogging.js.download" | 3 -- .../sharethis.js.download" | 3 -- .../site.min.css" | 3 -- .../site.min.js.download" | 3 -- .../tex-mml-chtml.js.download" | 3 -- .../trendmd.min.js.download" | 3 -- ...rs~ds~ps_f8279b26b9bf5f5ab409.js.download" | 3 -- assays/PeakCalling/dataset/README.md | 4 +-- 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sha256:732c169207e9f3d10a75f3708837f60a38ae529bce130530cf45f0e9735617d0 +size 5441 diff --git a/studies/ArchitectureAndProposedModels/resources/README.md b/studies/ArchitectureAndProposedModels/resources/README.md index 598fb0c..4f23ba3 100644 --- a/studies/ArchitectureAndProposedModels/resources/README.md +++ b/studies/ArchitectureAndProposedModels/resources/README.md @@ -4,4 +4,19 @@ ## Figure source -https://academic.oup.com/view-large/figure/464175134/vbae074f2.tif \ No newline at end of file +https://academic.oup.com/view-large/figure/464175134/vbae074f2.tif + +**Table 2.** Model architecture and dataset explanation (short). + +| **Model name** | **Dataset** | **Architecture** | | +|----------------------------|-------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------|---| +| U-Net | ATAC-seq | 3 convolutional layers + 3 transposed convolutional layers | | +| Hybrid | ATAC-seq | U-Net + 2 LSTM layers | | +| BiHybrid | ATAC-seq | U-Net + 2 BiLSTM layers | | +| BiHybrid_02 | ATAC-seq | U-Net + 2 BiLSTM layers + 6 batch normalization layers | | +| BiHybrid_03.1 (see Fig. 2) | ATAC-seq | U-Net + 2 BiLSTM layers + 6 batch normalization layers + 1 dropout layer (dropout probability of 0.3) | | +| BiHybrid_03.2 | ATAC-seq | U-Net + 2 BiLSTM layers + 6 batch normalization layers + 1 dropout layer (dropout probability of 0.5) | | +| BiHybrid_04 | ATAC-seq, filtered flagged sequences* | U-Net + 2 BiLSTM layers + 6 batch normalization layers + 1 dropout layer (dropout probability of 0.3) | | +| BiHybrid_05 | ChIP-seq (H3K4me3), filtered flagged sequences* | U-Net + 2 BiLSTM layers + 6 batch normalization layers + 1 dropout layer (dropout probability of 0.3) | | +| Combined | ATAC-seq, ChIP-seq (H3K4me3), filtered flagged sequences* | U-Net + 2 BiLSTM layers + 6 batch normalization layers + 1 dropout layer (dropout probability of 0.3) | | +| Combined_02 | ATAC-seq, ChIP-seq (H3K4me3), filtered flagged sequences* (+ additional data) | U-Net + 2 BiLSTM layers + 6 batch normalization layers + 1 dropout layer (dropout probability of 0.3) | | \ No newline at end of file diff --git a/studies/Data/resources/README.md b/studies/Data/resources/README.md index 0d109eb..171a172 100644 --- a/studies/Data/resources/README.md +++ b/studies/Data/resources/README.md @@ -6,3 +6,32 @@ https://academic.oup.com/view-large/figure/464175126/vbae074f1.tif +**Table 1.** Plant genomes and available datasets. + +| **Domain** | **Species** | **ATAC-seq** | **ChIP-seq (H3K4me3)** | +|------------|-----------------------------|--------------|------------------------| +| Algae | _Bigelowiella natans_ | ✔ | | +| | _Chlamydomonas reinhardtii_ | | ✔ | +| Mosses | _Marchantia polymorpha_ | ✔ | ✔ | +| Monocots | _Brachypodium distachyon_ | ✔ | ✔ | +| | _Eragrostis nindensis_ | ✔ | ✔ | +| | _Oropetium thomaeum_ | ✔ | | +| | _Oryza brachyantha_ | | ✔ | +| | _Oryza sativa_ | ✔ | ✔ | +| | _Panicum miliaceum_ | ✔ | | +| | _Setaria italica_ | | ✔ | +| | _Sorghum bicolor_ | ✔ | | +| | _Spirodela polyrhiza_ | ✔ | ✔ | +| | _Zea mays_ | ✔ | ✔ | +| Dicots | _Actinidia chinensis_ | ✔ | ✔ | +| | _Arabidopsis thaliana_ | ✔ | ✔ | +| | _Brassica napus_ | ✔ | ✔ | +| | _Brassica oleracea_ | | ✔ | +| | _Brassica rapa_ | | ✔ | +| | _Glycine max_ | ✔ | ✔ | +| | _Malus domestica_ | ✔ | ✔ | +| | _Medicago truncatula_ | ✔ | ✔ | +| | _Prunus persica_ | | ✔ | +| | _Pyrus x bretschneideri_ | | ✔ | +| | _Sesamum indicum_ | | ✔ | +| | _Solanum lycopersicum_ | ✔ | ✔ | \ No newline at end of file -- GitLab