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Quickstart: add the downstream analysis section (rest of #37 is on main) #40

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Merged
t0mdavid-m merged 5 commits into from
Oct 19, 2026
Merged

Quickstart: add the downstream analysis section (rest of #37 is on main) #40

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b90ef8a
Update quickstart with LFQ, TMT, and downstream analysis workflows
JKVISION1101 Sep 28, 2026
9e3db1d
Fix filtered PSM result directory lookup
JKVISION1101 Sep 28, 2026
f852064
Remove duplicate abundance result tabs
JKVISION1101 Sep 28, 2026
6131ea5
Clear stale downstream state when preprocessing results change
JKVISION1101 Sep 28, 2026
9fac122
Merge main; keep only the downstream analysis Quickstart section
claude Oct 19, 2026
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33 changes: 33 additions & 0 deletions content/quickstart.py
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Expand Up @@ -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 → Imputation → Normalization → Statistics → Plots/Pathway Analysis**.
"""
)

analysis_links = st.columns(4)
with analysis_links[0]:
st.page_link("content/filtering.py", label="Filtering", icon="🧹")
with analysis_links[1]:
st.page_link("content/imputation.py", label="Imputation", icon="🩹")
with analysis_links[2]:
st.page_link("content/normalization.py", label="Normalization", icon="⚖️")
with analysis_links[3]:
st.page_link("content/statistical.py", label="Statistics", icon="🔢")

st.markdown("## Workspaces")

st.markdown(
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