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a/assays/SpeciesSelection/dataset/README.md b/assays/SpeciesSelection/dataset/README.md index 5cf60a7496b150006b501bb5f4429feb1ae680a5..a47b74250dd6b03e4e99b19daed9b6dea03dccdd 100644 --- a/assays/SpeciesSelection/dataset/README.md +++ b/assays/SpeciesSelection/dataset/README.md @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ddd823f56ec8c8f6d5dfe25e3f43f8f40a614d76909c40cc268045102ec8fccf -size 982 +oid sha256:732c169207e9f3d10a75f3708837f60a38ae529bce130530cf45f0e9735617d0 +size 5441 diff --git a/studies/ArchitectureAndProposedModels/resources/README.md b/studies/ArchitectureAndProposedModels/resources/README.md index 598fb0c4e0d98769bf516599acf02a7c8394edee..4f23ba3fe9ed28c23d57fee5ebe590d1f50bff7e 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 0d109eb69013f7a02d9f84c32dd007f93dc1c4d1..171a17279ed36fd26356a6b8d78ee09cdb6281df 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