diff --git a/content/quickstart.py b/content/quickstart.py index 060beb1..48349f3 100644 --- a/content/quickstart.py +++ b/content/quickstart.py @@ -195,6 +195,39 @@ def render_windows_download_box(app_bytes: bytes) -> None: """ ) +st.markdown("### 5. Run Differential Protein Analysis") + +st.markdown( + """ +After quantification, continue through the downstream analysis pages in order: + +| Step | Available analysis | +|------|--------------------| +| **1. Filtering** | Remove proteins with low abundance, low repeatability, or low variance | +| **2. Imputation** | Handle missing values using MAR mean/median strategies or MNAR small-value replacement | +| **3. Normalization** | Apply mathematical transformation, sample normalization, and optional row scaling | +| **4. Statistics** | Test group differences and apply BH, Bonferroni, or no multiple-testing correction | +| **Volcano** | Explore effect size and adjusted-significance thresholds | +| **PCA** | Inspect sample separation using high-variance proteins | +| **Heatmap** | View abundance patterns across proteins and samples | +| **Clustered Heatmap** | Explore hierarchically clustered proteins and samples | +| **Pathway Analysis** | Run GO enrichment on statistically significant proteins | + +Each preprocessing page uses the output of the preceding step when available. The recommended +order is **Filtering โ†’ Imputation โ†’ Normalization โ†’ Statistics โ†’ Plots/Pathway Analysis**. +""" +) + +analysis_links = st.columns(4) +with analysis_links[0]: + st.page_link("content/filtering.py", label="Filtering", icon="๐Ÿงน") +with analysis_links[1]: + st.page_link("content/imputation.py", label="Imputation", icon="๐Ÿฉน") +with analysis_links[2]: + st.page_link("content/normalization.py", label="Normalization", icon="โš–๏ธ") +with analysis_links[3]: + st.page_link("content/statistical.py", label="Statistics", icon="๐Ÿ”ข") + st.markdown("## Workspaces") st.markdown(