Dataset card: plain labels, gene symbols in italics, and formatting fixes

README.md

@@ -12,9 +12,9 @@ tags:
 - single-cell
 - snRNA-seq
 - microglia
-- Alzheimer's disease
+- alzheimers-disease
 - SEA-AD
-- monotonic relationships
+- monotonic-relationships
 size_categories:
 - 10K<n<100K
 ---
@@ -35,7 +35,7 @@ size_categories:
 <p align="center">
 • Example data of the R package <a href="https://github.com/kahkengwong/cepip">cepip</a>, loaded with <code>cepip_example()</code>.<br>
 • 24,463 Micro-PVM_3-SEAAD cells from 10 brain regions, the table of 84 donors, and the DEG matrices.<br>
-• With these files, the PVM_3 and HKG8 control arms of the CEP-IP with CMRF analysis of SEA-AD microglia can be reproduced.
+• With these files, the PVM_3 arm and the HKG8 control arm of the CEP-IP with CMRF analysis of SEA-AD microglia can be reproduced.
 </p>
 
 ## Quick Start
@@ -60,19 +60,19 @@ res
 
 ## Example Output
 
-Output of cepip on the 13,331 PVM_3 NeoC cells with the settings of the paper, drawn by [`readme_figure.R`](https://github.com/kahkengwong/cepip/blob/main/assets/readme_figure.R) of the cepip repository. The aims, methods, code, and results of each pair of panels are in the [worked example](https://github.com/kahkengwong/cepip#4-worked-example) of the cepip README. The notes below explain what each pair of panels means.
+Output of cepip on the 13,331 PVM_3 NeoC cells with the settings of the paper, drawn by [`readme_figure.R`](https://github.com/kahkengwong/cepip/blob/main/assets/readme_figure.R) of the cepip repository. The aims, methods, code, and results of each pair of panels are in the [worked example](https://github.com/kahkengwong/cepip#4-worked-example) of the cepip README. The notes below explain each pair of panels.
 
 ### Panels A and B: SKCS-core Cells and the Inflection Point
 
 <p align="center"><img src="https://huggingface.co/datasets/kahkengwong/cepip_example/resolve/main/assets/cepip_example_AB.png" width="100%" alt="Panels A and B"></p>
 
-8,407 cells pass both SKCS gates (A). The residual GAM of the best-explained cells crosses zero at IP<sub>x</sub> = 2.4953, with an IPRS of 0.791 (B).
+In A, 8,407 cells pass both SKCS gates. The residual GAM of the best-explained cells crosses zero at IP<sub>x</sub> = 2.4953, with an IPRS of 0.791 (B).
 
 **(i) TREP and non-TREP cells.**
 - The number of TREP cells follows the deviance explained (DE) of the curve: they are the top round(n x DE) cells by EP.
 - TREP cells are the cells the curve explains best. Non-TREP cells (blue and red in A) follow the same trend but lie farther from the curve.
 
-**(ii) Why a second GAM.**
+**(ii) Reason for a second GAM.**
 - The first GAM is one smooth curve through all cells, so it averages over a change in the relationship.
 - The residuals of the best-explained cells show the change: these cells lie below the curve before the IP and above it after.
 - The second GAM gives these residuals a standard error, so the IP gets a 95% CI and IPRS can score how clear the crossing is.
@@ -81,13 +81,13 @@ Output of cepip on the 13,331 PVM_3 NeoC cells with the settings of the paper, d
 
 <p align="center"><img src="https://huggingface.co/datasets/kahkengwong/cepip_example/resolve/main/assets/cepip_example_CD.png" width="100%" alt="Panels C and D"></p>
 
-1,994 non-SKCS-core cells fall inside the band (C), and the gate keeps 1,351 of them as Recovered cells (D).
+In C, 1,994 non-SKCS-core cells fall inside the band, and the gate keeps 1,351 of them as Recovered cells (D).
 
-**(iii) Why the middle of the curve is lost.**
+**(iii) Loss of the middle of the curve.**
 - S<sub>i</sub> is the product of the two centered ranks of a cell. A cell near the middle rank of either gene therefore has S<sub>i</sub> close to 0, even when it lies on the curve.
 - The fixed S<sub>i</sub> gate removes this part of the curve (the gap in panel A). CMRF tests these cells by their distance to the curve instead.
 
-**(iv) What the gate protects against.**
+**(iv) Purpose of the gate.**
 - The candidates are kept only when the monotone curve fitted with them predicts held-out cells no worse than the curve of the reference cells alone, within its background variability.
 - Cells are removed from the farthest to the nearest, so the 643 removed candidates are the cells farthest from the curve.
 
@@ -95,7 +95,7 @@ Output of cepip on the 13,331 PVM_3 NeoC cells with the settings of the paper, d
 
 <p align="center"><img src="https://huggingface.co/datasets/kahkengwong/cepip_example/resolve/main/assets/cepip_example_EF.png" width="100%" alt="Panels E and F"></p>
 
-9,454 cells form the Module (E). In the pitcher plot, most Recovered cells lie left of the S<sub>i</sub> gate line (F).
+In E, 9,454 cells form the Module. In the pitcher plot, most Recovered cells lie left of the S<sub>i</sub> gate line (F).
 
 **(v) Use of the Module.**
 - The Module, split at the IP into Pre-IP and Post-IP cells, is the unit of the downstream steps: the share of each donor's cells in each group (`cepip_donor()`), the DEGs between groups (`cepip_deg()`), and the association of a donor share with outcomes (`cepip_associate()`). In the SEA-AD paper, the donor share of Module Post-IP cells was associated with worse cognition.
@@ -110,9 +110,9 @@ Output of cepip on the 13,331 PVM_3 NeoC cells with the settings of the paper, d
 
 | File | Rows x columns | Contents |
 |---|---|---|
-| `pvm3_cells.csv` | 24,463 x 23 | Micro-PVM_3-SEAAD cells with MT-CO3 > 0 (NeoC 13,331; NonNeoC 11,132): barcode, region set, region, donor, MT-CO3, the eight mitochondrial partner genes, `composite_part8` (the composite of the data export, single precision), ACTB, and the eight other housekeeping genes |
-| `hkg8_cells.csv` | 2,511 x 14 | Cells of the HKG8 control arm (NeoC 1,432; NonNeoC 1,079): ACTB, the eight housekeeping genes, and `composite_part8` |
-| `donors.csv` | 84 x 18 | Cognitive status, MMSE, CASI, CERAD, Braak, Thal, ADNC, CAA, APOE e4 dose, age at death, sex, PMI, RIN, brain pH, fresh brain weight, and the total Micro-PVM_3-SEAAD cells per donor and region set |
+| `pvm3_cells.csv` | 24,463 x 23 | Micro-PVM_3-SEAAD cells with *MT-CO3* > 0 (NeoC 13,331; NonNeoC 11,132): barcode, region set, region, donor, *MT-CO3*, the eight mitochondrial partner genes, `composite_part8` (the composite of the data export, single precision), *ACTB*, and the eight other housekeeping genes |
+| `hkg8_cells.csv` | 2,511 x 14 | Cells of the HKG8 control arm (NeoC 1,432; NonNeoC 1,079): *ACTB*, the eight housekeeping genes, and `composite_part8` |
+| `donors.csv` | 84 x 18 | Cognitive status, MMSE, CASI, CERAD, Braak, Thal, ADNC, CAA, *APOE* ε4 dose, age at death, sex, PMI, RIN, brain pH, fresh brain weight, and the total Micro-PVM_3-SEAAD cells per donor and region set |
 | `pvm3_deg_NeoC.rds` | 20,654 genes x 13,331 cells | Sparse matrix of the NeoC PVM_3 cells for `cepip_deg()` (genes expressed in at least 40 cells) |
 | `pvm3_deg_NonNeoC.rds` | 19,449 genes x 11,132 cells | The same for the NonNeoC PVM_3 cells |
 | `build_deg_matrices.R` | | Script that built the two DEG matrices |
@@ -121,11 +121,11 @@ The five data files are 82.8 MB in total. `cepip_example()` takes the names `"pv
 
 ## Data Details
 
-- **Expression values.** ln(CP10K + 1) from the SEA-AD multiregion release of 22 June 2026.
+- **Expression values.** ln(CP10K + 1) from the SEA-AD Multiregion release of 22 June 2026.
 - **Region sets.** NeoC (neocortical): DFC, MTG, AnG, STG, V1C, and ITG. NonNeoC (non-neocortical): HIP, MEC, LEC, and FI.
-- **Gene of interest.** MT-CO3.
-- **Partner genes.** MT-ATP6, MT-CO2, MT-ND3, MT-ND4, MT-CYB, MT-ND1, MT-ND2, and MT-CO1.
-- **HKG8 control arm.** ACTB against eight other housekeeping genes, in the ACTB > 0 cells of the M4 arm of the paper.
+- **Gene of interest.** *MT-CO3*.
+- **Partner genes.** *MT-ATP6*, *MT-CO2*, *MT-ND3*, *MT-ND4*, *MT-CYB*, *MT-ND1*, *MT-ND2*, and *MT-CO1*.
+- **HKG8 control arm.** *ACTB* against eight other housekeeping genes, in the *ACTB* > 0 cells of the M4 arm of the paper.
 
 ## Reproduced Values
 
@@ -134,7 +134,7 @@ The reproducibility script of cepip runs the PVM_3 arm, the HKG8 control arm, an
 | Value | PVM_3 NeoC | PVM_3 NonNeoC | HKG8 NeoC | HKG8 NonNeoC |
 |---|---|---|---|---|
 | Cells | 13,331 | 11,132 | 1,432 | 1,079 |
-| IPx | 2.4953 | 2.6572 | 1.5552 | 1.8130 |
+| IP<sub>x</sub> | 2.4953 | 2.6572 | 1.5552 | 1.8130 |
 | IPRS | 0.791 | 0.819 | 0.639 | 0.571 |
 | SKCS-core cells | 8,407 | 6,941 | 250 | 199 |
 | OriRef / Recovered | 8,103 / 1,351 | 6,646 / 1,089 | 239 / 287 | 191 / 240 |