diff --git a/poetry.lock b/poetry.lock
index 39ef393..7906464 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -6,22 +6,6 @@ category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "attrs"
-version = "22.2.0"
-description = "Classes Without Boilerplate"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-cov = ["attrs", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs"]
-docs = ["furo", "sphinx", "myst-parser", "zope.interface", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"]
-tests = ["attrs", "zope.interface"]
-tests-no-zope = ["hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist", "cloudpickle", "mypy (>=0.971,<0.990)", "pytest-mypy-plugins"]
-tests_no_zope = ["hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist", "cloudpickle", "mypy (>=0.971,<0.990)", "pytest-mypy-plugins"]
-
 [[package]]
 name = "black"
 version = "20.8b1"
@@ -106,15 +90,15 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.10.0"
+version = "3.12.0"
 description = "A platform independent file lock."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)", "sphinx (>=6.1.3)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.1)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)", "pytest (>=7.2.2)"]
+docs = ["furo (>=2023.3.27)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)", "sphinx (>=6.1.3)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "diff-cover (>=7.5)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)", "pytest (>=7.3.1)"]
 
 [[package]]
 name = "flake8"
@@ -158,7 +142,7 @@ six = "*"
 
 [[package]]
 name = "identify"
-version = "2.5.21"
+version = "2.5.22"
 description = "File identification library for Python"
 category = "dev"
 optional = false
@@ -169,7 +153,7 @@ license = ["ukkonen"]
 
 [[package]]
 name = "importlib-metadata"
-version = "6.0.0"
+version = "6.6.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -246,7 +230,7 @@ python-versions = ">=3.8"
 
 [[package]]
 name = "packaging"
-version = "23.0"
+version = "23.1"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
@@ -296,7 +280,7 @@ test = ["pytest", "pytest-cov", "scipy"]
 
 [[package]]
 name = "platformdirs"
-version = "3.1.1"
+version = "3.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
@@ -304,7 +288,7 @@ python-versions = ">=3.7"
 
 [package.extras]
 docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)", "sphinx (>=6.1.3)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2.1)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2.2)"]
 
 [[package]]
 name = "pluggy"
@@ -351,14 +335,13 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "pytest"
-version = "7.2.2"
+version = "7.3.1"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
@@ -367,7 +350,7 @@ pluggy = ">=0.12,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
 [[package]]
 name = "python-dateutil"
@@ -382,7 +365,7 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2022.7.1"
+version = "2023.3"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
@@ -398,11 +381,11 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "regex"
-version = "2022.10.31"
+version = "2023.3.23"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 
 [[package]]
 name = "ruff"
@@ -507,7 +490,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "virtualenv"
-version = "20.21.0"
+version = "20.22.0"
 description = "Virtual Python Environment builder"
 category = "dev"
 optional = false
@@ -515,12 +498,12 @@ python-versions = ">=3.7"
 
 [package.dependencies]
 distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<4"
+filelock = ">=3.11,<4"
+platformdirs = ">=3.2,<4"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=6.1.3)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.2.2)", "coverage-enable-subprocess (>=1)", "coverage (>=7.1)", "flaky (>=3.7)", "packaging (>=23)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "pytest (>=7.2.1)"]
+docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=6.1.3)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
+test = ["covdefaults (>=2.3)", "coverage-enable-subprocess (>=1)", "coverage (>=7.2.3)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "pytest (>=7.3.1)"]
 
 [[package]]
 name = "zipp"
@@ -544,7 +527,6 @@ appdirs = [
     {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
 ]
-attrs = []
 black = [
     {file = "black-20.8b1.tar.gz", hash = "sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea"},
 ]
@@ -552,7 +534,10 @@ cfgv = [
     {file = "cfgv-3.3.1-py2.py3-none-any.whl", hash = "sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426"},
     {file = "cfgv-3.3.1.tar.gz", hash = "sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736"},
 ]
-click = []
+click = [
+    {file = "click-8.0.4-py3-none-any.whl", hash = "sha256:6a7a62563bbfabfda3a38f3023a1db4a35978c0abd76f6c9605ecd6554d6d9b1"},
+    {file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"},
+]
 click-help-colors = [
     {file = "click-help-colors-0.9.1.tar.gz", hash = "sha256:78cbcf30cfa81c5fc2a52f49220121e1a8190cd19197d9245997605d3405824d"},
     {file = "click_help_colors-0.9.1-py3-none-any.whl", hash = "sha256:25a6bd22d8abbc72c18a416a1cf21ab65b6120bee48e9637829666cbad22d51d"},
@@ -566,7 +551,10 @@ flake8-builtins = [
     {file = "flake8-builtins-1.5.3.tar.gz", hash = "sha256:09998853b2405e98e61d2ff3027c47033adbdc17f9fe44ca58443d876eb00f3b"},
     {file = "flake8_builtins-1.5.3-py2.py3-none-any.whl", hash = "sha256:7706babee43879320376861897e5d1468e396a40b8918ed7bccf70e5f90b8687"},
 ]
-flake8-print = []
+flake8-print = [
+    {file = "flake8-print-4.0.1.tar.gz", hash = "sha256:12b3c3bf65329d8ca9acde949fb3b932ec113e9e5ffa6cb7cd55a7dbcd67dae1"},
+    {file = "flake8_print-4.0.1-py3-none-any.whl", hash = "sha256:e246bcd5b07d5259af460b7eff148052c49114640380d7f22340f30920fabf02"},
+]
 identify = []
 importlib-metadata = []
 iniconfig = []
diff --git a/scbs/diff.py b/scbs/diff.py
index 67061c2..2f49c64 100755
--- a/scbs/diff.py
+++ b/scbs/diff.py
@@ -38,7 +38,7 @@ def permuted_indices(idx_celltypes, celltype_1, celltype_2, total_cells):
     return index_g1, index_g2
 
 
-# @njit("float64(boolean)")
+@njit
 def calc_fdr(bools):
     """
     Calculates an adjusted p-value for each DMR using the Benjamini-Hochberg method.
@@ -46,15 +46,15 @@ def calc_fdr(bools):
     The array is sorted by absolute t-statistic and the boolean indicates whether the
     the DMR was found in a permutation (False) or in the real comparison (True).
     """
-    n_t = sum(bools)  # number of DMRs in the real comparison
+    n_t = bools.sum()  # number of DMRs in the real comparison
     n_t_null = len(bools) - n_t  # number of DMRs in the permutation
     fdisc = 0  # number of false discoveries up until a certain threshold
     tdisc = 0
     adj_p_vals = np.empty(bools.shape, dtype=np.float64)
     for i in range(len(bools)):
-        if bools[i]:
+        if bools[i]:  # it's from the real comparison
             tdisc += 1
-        else:
+        else:  # it's from the permutation
             fdisc += 1
         adj_p_val = (fdisc / n_t_null) / (tdisc / n_t)
         adj_p_vals[i] = adj_p_val