docs: clarify differential methods and contribution forms

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,57 @@
+name: Bug report
+description: Something in MetaManifold does not work as documented.
+labels: [bug]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Search the existing issues first. Raise issues about a fork's own code on that fork.
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps or command
+      description: The command you ran, or the steps in the web interface, so that someone else can repeat them.
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: What you expected
+    validations:
+      required: true
+  - type: textarea
+    id: actual
+    attributes:
+      label: What happened
+      description: Include the error message, the server log lines, or a screenshot.
+    validations:
+      required: true
+  - type: input
+    id: julia
+    attributes:
+      label: Julia version
+      placeholder: output of `julia --version`
+    validations:
+      required: true
+  - type: input
+    id: r
+    attributes:
+      label: R version
+      description: Only if the problem touches the R runtime; leave empty if you do not know it.
+      placeholder: output of `R --version | head -1`
+  - type: input
+    id: browser
+    attributes:
+      label: Browser and version
+      description: Only for problems in the web interface; leave empty for command-line reports.
+  - type: input
+    id: commit
+    attributes:
+      label: MetaManifold commit
+      placeholder: output of `git rev-parse --short HEAD`
+  - type: textarea
+    id: config
+    attributes:
+      label: Relevant configuration
+      description: The keys from `pipeline.yml` or the run's `run_config.yml` that bear on the problem.
+      render: yaml

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest a new feature or a change to an existing one.
+labels: [enhancement]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Search the existing issues first. To change an architectural decision, describe the change
+        here before writing any code. The settled decisions in CONTRIBUTING.md can be discussed in an
+        issue, but a pull request does not reopen them.
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem
+      description: What you are trying to do, and what stops you now.
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed change
+      description: What MetaManifold should do instead. For a statistical method, name the method and a reference for it.
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+  - type: dropdown
+    id: area
+    attributes:
+      label: Area
+      options:
+        - Pipeline stages
+        - Analysis and statistics
+        - Web interface
+        - Configuration
+        - Installation and toolchain
+        - Other
+    validations:
+      required: true

.github/pull_request_template.md

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+## Change and reason
+
+<!-- One logical change. Link relevant issues without claiming to close unrelated work. -->
+
+## Validation
+
+<!-- Exact commands, results, and Julia/R/bun versions actually tested.
+     State explicitly what was not run. -->
+
+## Scope
+
+<!-- What related work is left out? Explain any necessary lockfile change. -->
+
+## Contribution checks
+
+- [ ] I followed [CONTRIBUTING.md](https://github.com/JoshuaJewell/MetaManifold-WebUI/blob/main/CONTRIBUTING.md).
+- [ ] This branch starts at current upstream main and contains no merges from fork main.
+- [ ] CI has run and passes.
+- [ ] Existing licensing, citation and acknowledgement text is unchanged.

README.md

@@ -240,6 +240,40 @@ The composition view classifies each ASV/OTU into a biological category and rend
   <img src=".github/screenshots/composition.png" width="800" alt="Organism-category composition of two runs as stacked bars">
 </p>
 
+### Differential abundance
+
+In a study's analysis workspace, select two conditions (runs or pooled-run
+subgroups), a results table and a shared taxonomic rank. The first condition
+is the reference. Counts are aggregated by taxon after applicable
+`analysis.exclude_categories` filters. This workspace does not pass sample
+read-count bounds to the differential-abundance request, so those bounds do
+not exclude samples from this analysis.
+
+All `analysis.differential` options below (`method`, `offset`,
+`min_prevalence` and `replacement_delta`) are resolved at study scope.
+Set them in the study configuration; group and run overrides are not used
+by this endpoint, including when called from a group Analysis workspace.
+
+`analysis.differential.method` chooses the method:
+
+- `nb_glm` (default): a negative-binomial GLM per taxon using `MASS::glm.nb`,
+  with a library-size offset. The effect is log2 fold change; positive values
+  indicate greater abundance in the second condition. `offset` selects `tss`
+  (default) or `rle` scaling.
+- `clr_welch`: Welch's t-test on centred log-ratios after multiplicative zero
+  replacement with `zCompositions::cmultRepl`. The effect is a CLR difference,
+  not a fold change. `replacement_delta` controls the replacement fraction
+  (default 0.65); `offset` is not used.
+
+For either method, `min_prevalence` (default 0) filters taxa by the fraction of
+samples with nonzero counts. Benjamini–Hochberg adjustment includes only taxa
+that produced a p-value. Failed or filtered taxa have no substitute p-value;
+inspect their status and note in the results table. Invalid input or an
+unavailable required R package produces an explicit error.
+
+Implementation and reference tests: `src/analysis/differential.jl`,
+`src/server/routes/analysis.jl`, and `test/unit/test_differential.jl`.
+
 ### Figures and report
 
 The Figures tab lays analysis charts out on a page (A4, letter or a journal