diff --git a/Cargo.lock b/Cargo.lock
index 6c0eea9..780847a 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -9,7 +9,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8b79b82693f705137f8fb9b37871d99e4f9a7df12b917eed79c3d3954830a60b"
 dependencies = [
  "cfg-if",
- "getrandom",
+ "getrandom 0.2.12",
  "once_cell",
  "version_check",
  "zerocopy",
@@ -214,6 +214,18 @@ dependencies = [
  "wasi",
 ]
 
+[[package]]
+name = "getrandom"
+version = "0.3.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "899def5c37c4fd7b2664648c28120ecec138e4d395b459e5ca34f9cce2dd77fd"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "r-efi",
+ "wasip2",
+]
+
 [[package]]
 name = "heck"
 version = "0.4.1"
@@ -257,9 +269,9 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
 
 [[package]]
 name = "libc"
-version = "0.2.153"
+version = "0.2.189"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
+checksum = "3eaf3ede3fee6db1a4c2ee091bf8a8b4dccdc6d17f656fb07896ee72867612f2"
 
 [[package]]
 name = "libm"
@@ -295,7 +307,7 @@ dependencies = [
  "num-complex",
  "num-rational",
  "num-traits",
- "rand",
+ "rand 0.8.5",
  "rand_distr",
  "simba",
  "typenum",
@@ -420,6 +432,12 @@ dependencies = [
  "proc-macro2",
 ]
 
+[[package]]
+name = "r-efi"
+version = "5.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "69cdb34c158ceb288df11e18b4bd39de994f6657d83847bdffdbd7f346754b0f"
+
 [[package]]
 name = "rand"
 version = "0.8.5"
@@ -427,8 +445,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404"
 dependencies = [
  "libc",
- "rand_chacha",
- "rand_core",
+ "rand_chacha 0.3.1",
+ "rand_core 0.6.4",
+]
+
+[[package]]
+name = "rand"
+version = "0.9.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b9ef1d0d795eb7d84685bca4f72f3649f064e6641543d3a8c415898726a57b41"
+dependencies = [
+ "rand_chacha 0.9.0",
+ "rand_core 0.9.5",
 ]
 
 [[package]]
@@ -438,7 +466,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
 dependencies = [
  "ppv-lite86",
- "rand_core",
+ "rand_core 0.6.4",
+]
+
+[[package]]
+name = "rand_chacha"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb"
+dependencies = [
+ "ppv-lite86",
+ "rand_core 0.9.5",
 ]
 
 [[package]]
@@ -447,7 +485,16 @@ version = "0.6.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.12",
+]
+
+[[package]]
+name = "rand_core"
+version = "0.9.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "76afc826de14238e6e8c374ddcc1fa19e374fd8dd986b0d2af0d02377261d83c"
+dependencies = [
+ "getrandom 0.3.4",
 ]
 
 [[package]]
@@ -457,7 +504,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31"
 dependencies = [
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -555,7 +602,7 @@ dependencies = [
  "lazy_static",
  "nalgebra",
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -626,6 +673,15 @@ version = "0.11.0+wasi-snapshot-preview1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
+[[package]]
+name = "wasip2"
+version = "1.0.4+wasi-0.2.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b67efb37e106e55ce722a510d6b5f9c17f083e5fc79afc2badeb12cc313d9487"
+dependencies = [
+ "wit-bindgen",
+]
+
 [[package]]
 name = "webgestalt"
 version = "0.3.2"
@@ -645,7 +701,7 @@ dependencies = [
  "csv",
  "ndarray",
  "pretty_assertions",
- "rand",
+ "rand 0.9.5",
  "rayon",
  "serde",
  "serde_json",
@@ -728,6 +784,12 @@ version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8"
 
+[[package]]
+name = "wit-bindgen"
+version = "0.57.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1ebf944e87a7c253233ad6766e082e3cd714b5d03812acc24c318f549614536e"
+
 [[package]]
 name = "yansi"
 version = "0.5.1"
diff --git a/webgestalt_lib/Cargo.toml b/webgestalt_lib/Cargo.toml
index 9dc3c38..0ed4863 100644
--- a/webgestalt_lib/Cargo.toml
+++ b/webgestalt_lib/Cargo.toml
@@ -13,7 +13,7 @@ repository = "https://github.com/bzhanglab/webgestalt_rust"
 [dependencies]
 csv = "1.3.0"
 serde = { version = "1.0.190", features = ["std", "derive"] }
-rand = { version = "0.8.5", features = ["small_rng"] }
+rand = { version = "0.9.3", features = ["small_rng"] }
 rayon = "1.8.0"
 statrs = "0.16.0"
 ahash = "0.8.6"
diff --git a/webgestalt_lib/src/methods/gsea.rs b/webgestalt_lib/src/methods/gsea.rs
index cbce051..2243f42 100644
--- a/webgestalt_lib/src/methods/gsea.rs
+++ b/webgestalt_lib/src/methods/gsea.rs
@@ -421,9 +421,17 @@ pub fn gsea(
 /// ```
 pub fn make_permutations(permutations: i32, max: usize, seed: Option<u64>) -> Vec<Vec<usize>> {
     let mut temp_permutations: Vec<Vec<usize>> = Vec::new();
+    // `from_os_rng` is rand 0.9's name for what was `from_entropy`.
+    //
+    // Note that 0.9 changed what a seed *means*: it reimplemented
+    // `SmallRng::seed_from_u64` and replaced the `shuffle` algorithm, both listed under
+    // "Reproducibility-breaking changes". A given seed therefore produces different
+    // permutations here than it did under 0.8, and so different p-values. Verified rather
+    // than assumed — seed 42 gives [16, 2, 5, 14, …] under 0.8 and [16, 17, 19, 6, …] here.
+    // Seeds are comparable within a version of this crate, not across versions.
     let mut smallrng = match seed {
         Some(s) => rand::rngs::SmallRng::seed_from_u64(s),
-        None => rand::rngs::SmallRng::from_entropy(),
+        None => rand::rngs::SmallRng::from_os_rng(),
     };
     (0..permutations).for_each(|_i| {
         // get random permutations that are shared for all analyte sets