Update README.md

README.md

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----
-license: mit
----
+---
+license: mit
+language:
+- en
+tags:
+- genomics
+- yeast
+- transcription
+- perturbation
+- response
+- overexpression
+pretty_name: Hackett, 2020 Overexpression
+size_categories:
+- 1M<n<10M
+dataset_info:
+  features:
+    - name: target_locus_tag
+      dtype: string
+      description: The feature to which the effect/pvalue is assigned. See hf/BrentLab/yeast_genome_resources
+    - name: green_median
+      dtype: float
+      description: median of green (reference) channel fluorescence
+    - name: red_median
+      dtype: float
+      description: median of red (experimental) channel fluorescence
+    - name: log2_ratio
+      dtype: float
+      description: log2(red / green) subtracting value at time zero
+    - name: log2_cleaned_ratio
+      dtype: float
+      description: Non-specific stress response and prominent outliers removed
+    - name: log2_noise_model
+      dtype: float
+      description: estimated noise standard deviation
+    - name: log2_cleaned_ratio_zth2d
+      dtype: float
+      description: cleaned timecourses hard-thresholded based on multiple observations (or last observation) passing the noise model
+    - name: log2_selected_timecourses
+      dtype: float
+      description: cleaned timecourses hard-thresholded based on single observations passing noise model and impulse evaluation of biological feasibility
+    - name: log2_shrunken_timecourses
+      dtype: float
+      description: selected timecourses with observation-level shrinkage based on local FDR (false discovery rate). Most users of the data will want to use this column.
+  partitioning:
+    keys:
+      - name: regulator_symbol
+        dtype: string
+        levels:
+          - YER045C
+          - YLR131C
+          - YDR448W
+          - YDR216W
+          - YGL071W
+          - YPL202C
+          - YMR042W
+          - YML099C
+          - YDR421W
+          - YPR199C
+          - YKL185W
+          - YOR113W
+          - YKR099W
+          - YDL070W
+          - YER177W
+          - YDR423C
+          - YPL048W
+          - YMR280C
+          - YJR060W
+          - YLR418C
+          - YLR098C
+          - YOR028C
+          - YDR223W
+          - YNL027W
+          - YNR010W
+          - YIL036W
+          - YPL181W
+          - YOL145C
+          - YGL166W
+          - YPL177C
+          - YKR034W
+          - YIR023W
+          - YNL314W
+          - YPL049C
+          - YDR480W
+          - YGL043W
+          - YLR228C
+          - YBR239C
+          - YNL023C
+          - YPR104C
+          - YIL131C
+          - YNL068C
+          - YER109C
+          - YGL254W
+          - YOL051W
+          - YPL248C
+          - YML051W
+          - YMR136W
+          - YLR013W
+          - YIR013C
+          - YEL009C
+          - YGR252W
+          - YPL075W
+          - YNL199C
+          - GEV
+          - YDR096W
+          - YER040W
+          - YDR098C
+          - YER174C
+          - YJL103C
+          - YGL181W
+          - YJL110C
+          - YPR008W
+          - YFL031W
+          - YLR256W
+          - YGL237C
+          - YBL021C
+          - YKL109W
+          - YOR358W
+          - YCR065W
+          - YPL254W
+          - YBL008W
+          - YOR038C
+          - YJR140C
+          - YCR097W
+          - YOR032C
+          - YMR172W
+          - YJR094C
+          - YOL108C
+          - YCL055W
+          - YGR040W
+          - YOR123C
+          - YLR451W
+          - YLR011W
+          - YDR034C
+          - YMR021C
+          - YDL056W
+          - YDL005C
+          - YIR017C
+          - YPL038W
+          - YDR253C
+          - YNL103W
+          - YGR249W
+          - YGL035C
+          - YGL209W
+          - YER028C
+          - YMR070W
+          - YMR037C
+          - YKL062W
+          - YMR164C
+          - YMR228W
+          - YHR124W
+          - YDR043C
+          - YNR009W
+          - YAL051W
+          - YKR064W
+          - YHL020C
+          - YBR279W
+          - YGL013C
+          - YBL005W
+          - YLR266C
+          - YGL025C
+          - YKL043W
+          - YDL106C
+          - YFR034C
+          - YOR363C
+          - YLR014C
+          - YOR380W
+          - YPL133C
+          - YLR176C
+          - YMR182C
+          - YLR071C
+          - YKL038W
+          - YHL027W
+          - YPL089C
+          - YGR044C
+          - YPR065W
+          - YBL093C
+          - YNL330C
+          - YER169W
+          - YDL020C
+          - YBL025W
+          - YJR127C
+          - YGL244W
+          - YOL067C
+          - YGL252C
+          - YBL103C
+          - YOR140W
+          - YLR403W
+          - YCL010C
+          - YOL004W
+          - YNL236W
+          - YNL257C
+          - YJL089W
+          - YDL042C
+          - YHR206W
+          - YNL167C
+          - YBR182C
+          - YOR290C
+          - YBR289W
+          - YMR016C
+          - YOL148C
+          - YDR392W
+          - YGR063C
+          - YLR055C
+          - YHR041C
+          - YGR104C
+          - YCR081W
+          - YDR443C
+          - YNL309W
+          - YHR178W
+          - YHR084W
+          - YDR463W
+          - YHR006W
+          - YMR039C
+          - YDR310C
+          - YGL162W
+          - YPR009W
+          - YPL016W
+          - YDR146C
+          - YLR182W
+          - YCR042C
+          - YOR337W
+          - YBR083W
+          - YDR079C-A
+          - YDL080C
+          - YER184C
+          - YOR344C
+          - YOR295W
+          - YDL170W
+          - YPL139C
+          - YDR207C
+          - YDR213W
+          - YNL229C
+          - YPL230W
+          - YIL056W
+          - YML076C
+          - YOR083W
+          - YOR230W
+          - YOR229W
+          - YIL101C
+          - YML007W
+          - YHL009C
+          - YIR018W
+          - YDR259C
+          - YDR451C
+          - YLL054C
+          - YML027W
+          - YOR172W
+          - YOR162C
+          - Z3EV
+          - YJL056C
+          - YFL052W
+      - name: time
+        dtype: string
+        levels:
+          - 0
+          - 2
+          - 5
+          - 7
+          - 8
+          - 10
+          - 12
+          - 15
+          - 18
+          - 20
+          - 30
+          - 45
+          - 60
+          - 90
+          - 100
+          - 120
+          - 180
+          - 290
+      - name: mechanism
+        dtype: string
+        levels:
+          - GEV
+          - ZEV
+      - name: restriction
+        dtype: string
+        levels:
+          - M
+          - N
+          - P
+      - name: date
+        dtype: string
+        levels:
+          - 20150101
+          - 20150616
+          - 20150903
+          - 20151006
+          - 20151026
+          - 20151210
+          - 20151216
+          - 20160209
+          - 20160229
+          - 20160303
+          - 20160321
+          - 20160421
+          - 20160504
+          - 20160524
+          - 20160606
+          - 20160628
+          - 20160801
+          - 20160823
+          - 20160921
+          - 20161006
+          - 20161101
+          - 20161103
+          - 20161117
+      - name: strain
+        dtype: string
+        levels:
+          - SMY10
+          - SMY104
+          - SMY108
+          - SMY108n
+          - SMY110
+          - SMY113
+          - SMY117
+          - SMY117n
+          - SMY124
+          - SMY125
+          - SMY128
+          - SMY141
+          - SMY143
+          - SMY146
+          - SMY153
+          - SMY155
+          - SMY156
+          - SMY156n
+          - SMY159
+          - SMY170
+          - SMY179
+          - SMY181
+          - SMY19
+          - SMY196
+          - SMY2035
+          - SMY2049
+          - SMY2052
+          - SMY2055
+          - SMY2056
+          - SMY2057
+          - SMY2058
+          - SMY2059
+          - SMY2060
+          - SMY2061
+          - SMY2062
+          - SMY2063
+          - SMY2066
+          - SMY2067
+          - SMY2069
+          - SMY2071
+          - SMY2073
+          - SMY2074
+          - SMY2075
+          - SMY2076
+          - SMY2077
+          - SMY2078
+          - SMY2081
+          - SMY2082
+          - SMY2083
+          - SMY2085
+          - SMY2086
+          - SMY2087
+          - SMY2088
+          - SMY2092
+          - SMY2094
+          - SMY2096
+          - SMY2099
+          - SMY2100
+          - SMY2101
+          - SMY2103
+          - SMY2104
+          - SMY2105
+          - SMY2106
+          - SMY2107
+          - SMY2108
+          - SMY2109
+          - SMY2110
+          - SMY2111
+          - SMY2112
+          - SMY2113
+          - SMY2114
+          - SMY2115
+          - SMY2116
+          - SMY2118
+          - SMY2119
+          - SMY2120
+          - SMY2121
+          - SMY2123
+          - SMY2124
+          - SMY2125
+          - SMY2126
+          - SMY2127
+          - SMY2129
+          - SMY2132
+          - SMY2141
+          - SMY2143
+          - SMY2145
+          - SMY2146
+          - SMY2147
+          - SMY2148
+          - SMY2149
+          - SMY2150
+          - SMY2151
+          - SMY2152
+          - SMY2153
+          - SMY2154
+          - SMY2155
+          - SMY2156
+          - SMY2157
+          - SMY2159
+          - SMY2160
+          - SMY2161
+          - SMY2162
+          - SMY2163
+          - SMY2164
+          - SMY2165
+          - SMY2166
+          - SMY2167
+          - SMY2168
+          - SMY2169
+          - SMY2170
+          - SMY2171
+          - SMY2173
+          - SMY2174
+          - SMY2175
+          - SMY2176
+          - SMY2177
+          - SMY2178
+          - SMY2179
+          - SMY2180
+          - SMY2181
+          - SMY2182
+          - SMY2183
+          - SMY2184
+          - SMY2185
+          - SMY2186
+          - SMY2187
+          - SMY2188
+          - SMY2189
+          - SMY2190
+          - SMY2191
+          - SMY2192
+          - SMY2193
+          - SMY2194
+          - SMY2195
+          - SMY2196
+          - SMY2197
+          - SMY22
+          - SMY2202
+          - SMY2203
+          - SMY2204
+          - SMY2205
+          - SMY2206
+          - SMY2207
+          - SMY2208
+          - SMY2209
+          - SMY2210
+          - SMY2211
+          - SMY2212
+          - SMY2213
+          - SMY2214
+          - SMY2215
+          - SMY2216
+          - SMY2217
+          - SMY2219
+          - SMY2220
+          - SMY2221
+          - SMY2222
+          - SMY2223
+          - SMY2224
+          - SMY2225
+          - SMY2226
+          - SMY2227
+          - SMY2228
+          - SMY2229
+          - SMY2230
+          - SMY2232
+          - SMY2233
+          - SMY2234
+          - SMY2235
+          - SMY2236
+          - SMY2237
+          - SMY2238
+          - SMY2239
+          - SMY2240
+          - SMY2241
+          - SMY2242
+          - SMY2243
+          - SMY2244
+          - SMY2245
+          - SMY2263
+          - SMY2264
+          - SMY2266a
+          - SMY2266b
+          - SMY2266c
+          - SMY2270
+          - SMY2273
+          - SMY254a
+          - SMY254c
+          - SMY257
+          - SMY26
+          - SMY27
+          - SMY39
+          - SMY40
+          - SMY41
+          - SMY42
+          - SMY44
+          - SMY54
+          - SMY55
+          - SMY57
+          - SMY58
+          - SMY59
+          - SMY62
+          - SMY64
+          - SMY69
+          - yRSM164
+          - yRSM170
+          - yRSM175
+          - yRSM204
+          - yRSM206
+          - yRSM209
+          - yRSM84
+          - yRSM86
+          - yRSM92
+          - YukoSMY2047
+configs:
+  - config_name: data
+    default: true
+    data_files:
+      - split: train
+        path:
+          - data/*/*/*/*/*/*/part-0.parquet
+---
+# Hackett 2020
+
+This Dataset is a parsed version of the data provided by [Calicolabs](https://idea.research.calicolabs.com/data)
+under the heading "Raw & processed gene expression data".
+
+
+[Hackett SR, Baltz EA, Coram M, Wranik BJ, Kim G, Baker A, Fan M, Hendrickson DG, Berndl M, McIsaac RS. Learning causal networks using inducible transcription factors and transcriptome-wide time series. Mol Syst Biol. 2020 Mar;16(3):e9174. doi: 10.15252/msb.20199174. PMID: 32181581; PMCID: PMC7076914.](https://doi.org/10.15252/msb.20199174)
+## Usage
+
+You may access just the Dataset metadata like this:
+
+```python
+from huggingface_hub import ModelCard
+
+card = ModelCard.load("BrentLab/hackett_2020", repo_type="dataset")
+
+# cast to dict
+card_dict = card.data.to_dict()
+
+# Get partition information
+card_dict.get("dataset_info").get("partitioning").get("keys")
+```
+
+Output:
+
+```raw
+
+```
+
+You can use this information to pull only the partition you're interested in, eg
+
+```python
+from huggingface_hub import hf_hub_download
+
+# Download a single partition file and store it in the local cache
+local_file = hf_hub_download(
+    repo_id="BrentLab/harbison_2004",
+    repo_type="dataset",
+    filename="data/condition=YPD/regulator_locus_tag=YER045C/part-0.parquet"
+)
+```
+
+<details>
+<summary><strong>Dataset Details</strong></summary>
+
+The data was extract from The [Young Lab's website](http://younglab.wi.mit.edu/regulatory_code/GWLD.html).
+
+I pulled the 'Excel' versions of both the P values (the downloaded file is called files_for_paper_abbr.zip)
+and Binding ratios (Ratio_forpaper_abbr.zip).  
+
+The following is copied from the [Young's lab explanation of the analysis](http://younglab.wi.mit.edu/regulatory_code/Analysis.html):  
+
+> The microarrays were scanned using an Axon200B scanner, and the images were analyzed with Genepix 5.0. Columns corresponding to the background
+> subtracted intensities and standard deviation of the background were extracted for further analysis. The intensities for the two channels, representing
+> the immunoprecipitated (test) and unenriched (control) samples, were normalized by using the median of each channel to calculate a normalization factor,
+> normalizing all datasets to a single median intensity. The log ratio of the intensity in the test channel to the control channel was calculated.
+> To account for biases in the immunoprecipitation reaction, these log ratios were normalized for each spot by subtracting the average log ratio of each
+> spot across all arrays. The intensities in the test channel were then adjusted to yield this normalized ratio. Finally, an error model was used to
+> calculate significance of enrichment on each chip and to combine data for replicates to obtain a final average ratio and significance of enrichment
+> for each intergenic region. Each intergenic region was assigned to the genes it is most likely to regulate.
+> We have included new refinements in our analysis relative to that used in Lee et al. Notably, we have excluded artefactual spots from analysis,
+> selected more reliable probes for normalization and assigned quality metrics to individual arrays to identify low quality experiments.
+
+The script used to parse this data from the data provided by the Young lab into the parquet dataset presented here is included in `scripts/`
+
+</details>
+
+<details>
+<summary><strong>Dataset Structure</strong></summary>
+
+### data/
+
+This is a **Parquet** dataset where the partitions are based on `condition` and `regulator_locus_tag`.
+Each row represents the effect and pvalue on a given target gene (`target_locus_tag`)
+
+| Field                 | Description                                                                                                                                                                                      |
+|-----------------------|-------------------------------------------------------------------------------------------------------------------------|
+| `condition`           | See below for a definition of each level                                                                                |
+| `regulator_locus_tag` | The systematic ID of the ChIP'ed regulator. See hf/BrentLab/yeast_genome_resources to map to the common name (symbol)   |
+| `target_locus_tag`    | the systematic ID of the feature to which the Young lab assigned the effect/pvalue                                      |
+| `effect`              | chip based binding ratio                                                                                                |
+| `pvalue`              | pvalue of the effect                                                                                                    |
+
+</details>
+
+**Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)