PyOVERCAST 1.0.0__tar.gz → 1.0.2__tar.gz

{pyovercast-1.0.0 → pyovercast-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyOVERCAST
-Version: 1.0.0
+Version: 1.0.2
 Summary: A Python package for mining key transcription factors from transcriptome data.
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT
@@ -17,19 +17,22 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy==1.26; sys_platform == "darwin"
+Requires-Dist: numpy>=1.26; sys_platform == "darwin"
 Requires-Dist: numpy>=2.0; sys_platform == "win32"
 Requires-Dist: numpy>=2.0; sys_platform == "linux"
-Requires-Dist: pandas==3.0; sys_platform == "darwin"
+Requires-Dist: pandas>=3.0; sys_platform == "darwin"
 Requires-Dist: pandas>=3.0; sys_platform == "win32"
 Requires-Dist: pandas>=3.0; sys_platform == "linux"
-Requires-Dist: statsmodels==0.14; sys_platform == "darwin"
+Requires-Dist: statsmodels>=0.14; sys_platform == "darwin"
 Requires-Dist: statsmodels>=0.14; sys_platform == "win32"
 Requires-Dist: statsmodels>=0.14; sys_platform == "linux"
-Requires-Dist: seaborn==0.13; sys_platform == "darwin"
+Requires-Dist: scipy>=1.16; sys_platform == "darwin"
+Requires-Dist: scipy>=1.16; sys_platform == "win32"
+Requires-Dist: scipy>=1.16; sys_platform == "linux"
+Requires-Dist: seaborn>=0.13; sys_platform == "darwin"
 Requires-Dist: seaborn>=0.13; sys_platform == "win32"
 Requires-Dist: seaborn>=0.13; sys_platform == "linux"
-Requires-Dist: matplotlib==3.11; sys_platform == "darwin"
+Requires-Dist: matplotlib>=3.11; sys_platform == "darwin"
 Requires-Dist: matplotlib>=3.11; sys_platform == "win32"
 Requires-Dist: matplotlib>=3.11; sys_platform == "linux"
 Provides-Extra: dev
@@ -45,7 +48,7 @@ A Python package for mining key transcription factors from transcriptome data.
 ## Installation
 
 ```bash
-pip install numpy pandas statsmodels seaborn matplotlib PyOVERCAST
+pip install numpy pandas statsmodels scipy seaborn matplotlib PyOVERCAST
 ```
 
 ## Usage
@@ -73,10 +76,10 @@ if __name__ == '__main__':
 	result = predict.olcr(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
 
 	# or predict one DEG-list with bootstrap
-	result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
+	result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
 
 	# save result to text file
-	result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8-sig')
+	result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
 	
 	# plot OLC matrix
 	predict.plot_olc(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)

{pyovercast-1.0.0 → pyovercast-1.0.2}/PyOVERCAST/predict.py

@@ -14,6 +14,8 @@ plt.rcParams['axes.unicode_minus'] = False  # 解决负号显示问题
 import multiprocessing as mp
 import seaborn as sns
 
+from scipy import stats
+
 overcast_data_dir = './OVERCAST_data'
 
 def read_tfbs_file(file, tfbs):
@@ -150,6 +152,114 @@ def compute_dtci_core(df, x_col='x', y_col='y', z_col='z',
 
 	return DTCI, beta_hat, R2_adj, p_values[3], model.resid
 
+def fitting_gaussian_dist(observations):
+	fig, ax = plt.subplots(figsize=(10, 6))
+
+	# 直方图
+	ax.hist(observations, bins=25, density=True, alpha=0.6, color='#4A90D9', 
+			edgecolor='white', label='obsvs hist')
+
+	# 目标观测值
+	x_target = 0.01
+
+	# 拟合的高斯分布曲线
+	mu_mle = np.mean(observations)
+	sigma_mle = np.std(observations, ddof=1)  # 无偏标准差
+
+	x_range = np.linspace(observations.min(), observations.max(), 500)
+	cdf_value = stats.norm.pdf(x_target, loc=mu_mle, scale=sigma_mle)
+	pdf_fitted = stats.norm.pdf(x_range, loc=mu_mle, scale=sigma_mle)
+	ax.plot(x_range, pdf_fitted, 'r-', linewidth=2.5, label=f'fitting Gaussian N({mu_mle:.2f}, {sigma_mle:.2f}^2)')
+
+	# 标记目标观测值
+	ax.axvline(x=x_target, color='#E74C3C', linestyle='--', linewidth=2, label=f'target values x = {x_target}')
+
+	# 填充CDF区域（x_target左侧）
+	x_fill = np.linspace(x_range.min(), x_target, 200)
+	pdf_fill = stats.norm.pdf(x_fill, loc=mu_mle, scale=sigma_mle)
+	ax.fill_between(x_fill, pdf_fill, alpha=0.3, color='#E74C3C', label=f'CDF = {cdf_value:.4f}')
+
+	'''
+	# 标注
+	ax.annotate(f'F({x_target}) = {cdf_value:.4f}\n≈ {cdf_value*100:.1f}%', 
+				xy=(x_target, stats.norm.pdf(x_target, mu_mle, sigma_mle)),
+				xytext=(x_target + 8, 0.035),
+				fontsize=12, color='#E74C3C',
+				arrowprops=dict(arrowstyle='->', color='#E74C3C', lw=1.5),
+				bbox=dict(boxstyle='round,pad=0.3', facecolor='#FFE5E5', edgecolor='#E74C3C'))
+	'''
+
+	ax.set_xlabel('observes', fontsize=12)
+	ax.set_ylabel('density function', fontsize=12)
+	ax.set_title('Gaussian fitting and CDFs', fontsize=14, fontweight='bold')
+	ax.legend(loc='upper left', fontsize=10)
+	ax.grid(True, alpha=0.3)
+
+	plt.tight_layout()
+	plt.savefig('gaussian_fitting_cdf.png', dpi=150, bbox_inches='tight')
+	plt.show()
+
+def fitting_gamma_dist(observations, x_target):
+	# ========== 1. 你的观测值（替换成你自己的数据） ==========
+	# 伽玛分布要求数据为正数
+	#observations = np.array([2.5, 3.1, 4.8, 5.2, 3.9, 6.1, 4.5, 5.8, 3.3, 4.0, 5.5, 4.2, 6.5, 3.7, 5.0, 4.6, 5.3, 3.2, 4.9, 5.1])
+	observations = observations[observations > 0]
+
+	# 目标观测值（必须 > 0）
+	#x_target = 5.0
+
+	# ========== 2. 拟合伽玛分布 ==========
+	# gamma.fit 返回 (shape, loc, scale)
+	# print(observations.min(), observations.max())
+	shape, loc, scale = stats.gamma.fit(observations, floc=0)  # floc=0 固定位置参数为0（标准两参数伽玛）
+
+	'''
+	print(f"样本量: {len(observations)}")
+	print(f"拟合的伽玛分布参数:")
+	print(f"  形状参数 (α/k) = {shape:.4f}")
+	print(f"  尺度参数 (θ)   = {scale:.4f}")
+	print(f"  位置参数 (loc) = {loc:.4f}")
+	'''
+
+	# 均值和方差的理论值
+	mean_gamma = shape * scale
+	var_gamma = shape * scale**2
+	# print(f"\n理论均值: {mean_gamma:.4f} (样本均值: {np.mean(observations):.4f})")
+	# print(f"理论方差: {var_gamma:.4f} (样本方差: {np.var(observations, ddof=1):.4f})")
+
+	# ========== 3. 计算 CDF ==========
+	cdf_value = stats.gamma.cdf(x_target, a=shape, loc=loc, scale=scale)
+	# print(f"\n观测值 x = {x_target} 的 CDF:")
+	# print(f"  F({x_target}) = P(X ≤ {x_target}) = {cdf_value:.6f}")
+	# print(f"  即约有 {cdf_value*100:.2f}% 的数据小于或等于 {x_target}")
+
+	'''
+	# ========== 4. 可视化 ==========
+	plt.figure(figsize=(10, 5))
+
+	# 直方图
+	plt.hist(observations, bins=12, density=True, alpha=0.6, color='steelblue', 
+			 edgecolor='white', label='观测值直方图')
+
+	# 拟合的伽玛分布曲线
+	x = np.linspace(observations.min(), observations.max(), 500)
+	pdf_fitted = stats.gamma.pdf(x, a=shape, loc=loc, scale=scale)
+	plt.plot(x, pdf_fitted, 'r-', lw=2.5, 
+			 label=f'拟合伽玛 Γ({shape:.2f}, {scale:.2f})')
+
+	# 标记目标值
+	plt.axvline(x_target, color='crimson', linestyle='--', lw=2, 
+				label=f'目标值 x = {x_target}')
+
+	# 填充 CDF 区域（目标值左侧）
+	x_fill = np.linspace(0.01, x_target, 200)
+	pdf_fill = stats.gamma.pdf(x_fill, a=shape, loc=loc, scale=scale)
+	plt.fill_between(x_fill, pdf_fill, alpha=0.3, color='crimson', 
+					 label=f'CDF = {cdf_value:.4f}')
+	plt.show()
+	'''
+	return cdf_value
+
 def bootstrap_parametric_h0(df, n_bootstrap=2000, random_state=42):
 	"""
 	参数化Bootstrap：在H0（无对角线趋势，即beta3=0）下生成数据
@@ -191,9 +301,11 @@ def bootstrap_parametric_h0(df, n_bootstrap=2000, random_state=42):
 			pass
 
 	dtci_null = np.array(dtci_null)
+	#fitting_gaussian_dist(dtci_null)
+	p_value = 1.0 - fitting_gamma_dist(dtci_null, dtci_obs)
 
 	# 步骤5：计算p值 (H1: DTCI > 0)
-	p_value = np.mean(dtci_null >= dtci_obs)
+	# p_value = np.mean(dtci_null >= dtci_obs)
 
 	return {
 		'method': '参数化Bootstrap (H0: beta3=0)',
@@ -374,7 +486,7 @@ def plot_fit3D_plot(df1, df2, win):
 	# df = Z_to_frame(rrho_df.to_numpy())
 	plot_3D_surface(rrho_df.to_numpy())
 
-def rrho_coor_bs(df1, df2, win):
+def rrho_coor_bs(df1, df2, win, bs_n):
 	gene_col1 = df1.columns[0]
 	score_col1 = df1.columns[1]
 	df1 = df1.sort_values(score_col1, ascending=False)
@@ -400,7 +512,7 @@ def rrho_coor_bs(df1, df2, win):
 
 	#beta_xy, pval_xy = td_coor(rrho_df.to_numpy())
 	df = Z_to_frame(rrho_df.to_numpy())
-	dtci_res = bootstrap_parametric_h0(df)
+	dtci_res = bootstrap_parametric_h0(df, n_bootstrap=bs_n)
 	beta_xy = dtci_res['beta3']
 	pval_xy = dtci_res['dtci_pval']
 	DTCI = dtci_res['dtci_obs']
@@ -422,17 +534,15 @@ def thread_one(tfbs_array, deg_list, win, shared_list, nn, lock):
 			nn[1] += 1
 			print(str(nn[1]) + ' / ' + str(nn[0]))
 
-def thread_one_bs(tfbs_array, deg_list, win, shared_list, nn, lock):
+def thread_one_bs(tfbs_array, deg_list, win, bs_n, shared_list, nn, lock):
 	tf_n = len(tfbs_array)
 	epsilon = 1e-15   # 常用值
 	for i in range(tf_n):
 		# fin_n += 1
-		beta_xy, pval_xy, DTCI, bs_pval = rrho_coor_bs(deg_list, tfbs_array[i][1], win)
-		#score = math.pow(abs(beta_xy), 1.0) * math.log10(pval_xy + epsilon) * -1.0
-		#if math.isnan(score):
-		#	score = 0
+		beta_xy, pval_xy, DTCI, bs_pval = rrho_coor_bs(deg_list, tfbs_array[i][1], win, bs_n)
+		rank_score = (DTCI * (-1.0 * math.log10(bs_pval + 1E-25) / 25)) ** 0.5
 		with lock:
-			shared_list.append([tfbs_array[i][0], beta_xy, pval_xy, DTCI, bs_pval])
+			shared_list.append([tfbs_array[i][0], beta_xy, pval_xy, DTCI, bs_pval, rank_score])
 			nn[1] += 1
 			print(str(nn[1]) + ' / ' + str(nn[0]))
 
@@ -504,7 +614,7 @@ def olcr(set_names=None, list_file=None, win=30, thread_n=16, data_dir=None):
 
 	return df
 
-def olcr_bootstrap(set_names=None, list_file=None, win=30, thread_n=16, data_dir=None):
+def olcr_bootstrap(set_names=None, list_file=None, win=30, thread_n=16, bs_n=2000, data_dir=None):
 	if data_dir == None:
 		data_dir = overcast_data_dir
 	if not (os.path.exists(data_dir) and os.path.isdir(data_dir)):
@@ -534,7 +644,7 @@ def olcr_bootstrap(set_names=None, list_file=None, win=30, thread_n=16, data_dir
 	tfbs_array_splits = split_into_n_even(tfbs_array, thread_n)
 	task_args = []
 	for ti in range(thread_n):
-		task_args.append((tfbs_array_splits[ti], deg_list, win, shared_list, nn, lock))
+		task_args.append((tfbs_array_splits[ti], deg_list, win, bs_n, shared_list, nn, lock))
 	
 	# 创建进程池
 	with mp.Pool(processes=thread_n) as pool:
@@ -547,18 +657,53 @@ def olcr_bootstrap(set_names=None, list_file=None, win=30, thread_n=16, data_dir
 	# 打印结果
 	print("time consumed:", elapsed)
 
-	sorted_results = sorted(shared_list, key=lambda x: (x[-1], -x[-2]), reverse=False) # lambda x: (x[4], -x[1]), reverse=False
+	#sorted_results = sorted(shared_list, key=lambda x: (x[-1], -x[-2]), reverse=False) # lambda x: (x[4], -x[1]), reverse=False
+	sorted_results = sorted(shared_list, key=lambda x: x[-1], reverse=True) # lambda x: (x[4], -x[1]), reverse=False
 	results = []
 	ln = len(sorted_results)
 	for li in range(len(sorted_results)):
 		ratio = (li + 1) / ln
-		rline = sorted_results[li] + [li + 1, ratio]
+		rline = sorted_results[li] + [ratio]
 		results.append(rline)
-	col_names = ['TF_motif', 'Beta3', 'Beta3_Pvalue', 'DTCI', 'DTCI_Pvalue', 'Rank', 'Rank / N']
+	col_names = ['TF_motif', 'Beta3', 'Beta3_Pvalue', 'DTCI', 'DTCI_Pvalue', 'Rank_Score', 'Rank / N']
 	df = pd.DataFrame(results, columns=col_names)
 
 	return df
 
+def olcr_bootstrap_1cpu(set_names=None, list_file=None, win=30, thread_n=16, bs_n=2000, data_dir=None):
+	if data_dir == None:
+		data_dir = overcast_data_dir
+	if not (os.path.exists(data_dir) and os.path.isdir(data_dir)):
+		print("OVERCAST_data folder can not found!")
+		exit(1)
+	sets_files = []
+	for set1 in set_names:
+		sets_file = data_dir + '/TF-target_sets/' + set1 + '.txt'
+		if not os.path.exists(sets_file):
+			print(sets_file, 'not exist!')
+			exit(1)
+		else:
+			sets_files.append(sets_file)
+	degl_file = list_file
+	if not os.path.exists(degl_file):
+		print(degl_file, 'not exist!')
+		exit(1)
+
+	tfbs_array = read_gene_sets(sets_files)
+	deg_list = read_DEG_list(degl_file)
+	
+	tf_n = len(tfbs_array)
+	epsilon = 1e-15   # 常用值
+	nn = [tf_n, 0]
+	for i in range(tf_n):
+		# fin_n += 1
+		beta_xy, pval_xy, DTCI, bs_pval = rrho_coor_bs(deg_list, tfbs_array[i][1], win, bs_n)
+		#score = math.pow(abs(beta_xy), 1.0) * math.log10(pval_xy + epsilon) * -1.0
+		#if math.isnan(score):
+		#	score = 0
+		nn[1] += 1
+		print(str(nn[1]) + ' / ' + str(nn[0]))
+
 def plot_olc(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8'], list_file='input_deg-list.txt', tf='NFKB1_HUMAN.H11MO.1.B', win=30, data_dir=None):
 	if data_dir == None:
 		data_dir = overcast_data_dir

{pyovercast-1.0.0 → pyovercast-1.0.2}/PyOVERCAST.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyOVERCAST
-Version: 1.0.0
+Version: 1.0.2
 Summary: A Python package for mining key transcription factors from transcriptome data.
 Author-email: Tinghua Huang <thua45@126.com>
 License-Expression: MIT
@@ -17,19 +17,22 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy==1.26; sys_platform == "darwin"
+Requires-Dist: numpy>=1.26; sys_platform == "darwin"
 Requires-Dist: numpy>=2.0; sys_platform == "win32"
 Requires-Dist: numpy>=2.0; sys_platform == "linux"
-Requires-Dist: pandas==3.0; sys_platform == "darwin"
+Requires-Dist: pandas>=3.0; sys_platform == "darwin"
 Requires-Dist: pandas>=3.0; sys_platform == "win32"
 Requires-Dist: pandas>=3.0; sys_platform == "linux"
-Requires-Dist: statsmodels==0.14; sys_platform == "darwin"
+Requires-Dist: statsmodels>=0.14; sys_platform == "darwin"
 Requires-Dist: statsmodels>=0.14; sys_platform == "win32"
 Requires-Dist: statsmodels>=0.14; sys_platform == "linux"
-Requires-Dist: seaborn==0.13; sys_platform == "darwin"
+Requires-Dist: scipy>=1.16; sys_platform == "darwin"
+Requires-Dist: scipy>=1.16; sys_platform == "win32"
+Requires-Dist: scipy>=1.16; sys_platform == "linux"
+Requires-Dist: seaborn>=0.13; sys_platform == "darwin"
 Requires-Dist: seaborn>=0.13; sys_platform == "win32"
 Requires-Dist: seaborn>=0.13; sys_platform == "linux"
-Requires-Dist: matplotlib==3.11; sys_platform == "darwin"
+Requires-Dist: matplotlib>=3.11; sys_platform == "darwin"
 Requires-Dist: matplotlib>=3.11; sys_platform == "win32"
 Requires-Dist: matplotlib>=3.11; sys_platform == "linux"
 Provides-Extra: dev
@@ -45,7 +48,7 @@ A Python package for mining key transcription factors from transcriptome data.
 ## Installation
 
 ```bash
-pip install numpy pandas statsmodels seaborn matplotlib PyOVERCAST
+pip install numpy pandas statsmodels scipy seaborn matplotlib PyOVERCAST
 ```
 
 ## Usage
@@ -73,10 +76,10 @@ if __name__ == '__main__':
 	result = predict.olcr(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
 
 	# or predict one DEG-list with bootstrap
-	result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
+	result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
 
 	# save result to text file
-	result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8-sig')
+	result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
 	
 	# plot OLC matrix
 	predict.plot_olc(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)

{pyovercast-1.0.0 → pyovercast-1.0.2}/PyOVERCAST.egg-info/requires.txt

@@ -1,15 +1,17 @@
 
 [:sys_platform == "darwin"]
-numpy==1.26
-pandas==3.0
-statsmodels==0.14
-seaborn==0.13
-matplotlib==3.11
+numpy>=1.26
+pandas>=3.0
+statsmodels>=0.14
+scipy>=1.16
+seaborn>=0.13
+matplotlib>=3.11
 
 [:sys_platform == "linux"]
 numpy>=2.0
 pandas>=3.0
 statsmodels>=0.14
+scipy>=1.16
 seaborn>=0.13
 matplotlib>=3.11
 
@@ -17,6 +19,7 @@ matplotlib>=3.11
 numpy>=2.0
 pandas>=3.0
 statsmodels>=0.14
+scipy>=1.16
 seaborn>=0.13
 matplotlib>=3.11
 

{pyovercast-1.0.0 → pyovercast-1.0.2}/README.md

@@ -5,7 +5,7 @@ A Python package for mining key transcription factors from transcriptome data.
 ## Installation
 
 ```bash
-pip install numpy pandas statsmodels seaborn matplotlib PyOVERCAST
+pip install numpy pandas statsmodels scipy seaborn matplotlib PyOVERCAST
 ```
 
 ## Usage
@@ -33,10 +33,10 @@ if __name__ == '__main__':
 	result = predict.olcr(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
 
 	# or predict one DEG-list with bootstrap
-	result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
+	result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
 
 	# save result to text file
-	result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8-sig')
+	result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
 	
 	# plot OLC matrix
 	predict.plot_olc(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)

{pyovercast-1.0.0 → pyovercast-1.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyOVERCAST"
-version = "1.0.0"
+version = "1.0.2"
 license = "MIT"  # SPDX expression
 description = "A Python package for mining key transcription factors from transcriptome data."
 readme = "README.md"
@@ -21,19 +21,22 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "numpy==1.26; sys_platform == 'darwin'",
+    "numpy>=1.26; sys_platform == 'darwin'",
     "numpy>=2.0; sys_platform == 'win32'",
     "numpy>=2.0; sys_platform == 'linux'",
-    "pandas==3.0; sys_platform == 'darwin'",
+    "pandas>=3.0; sys_platform == 'darwin'",
     "pandas>=3.0; sys_platform == 'win32'",
     "pandas>=3.0; sys_platform == 'linux'",
-    "statsmodels==0.14; sys_platform == 'darwin'",
+    "statsmodels>=0.14; sys_platform == 'darwin'",
     "statsmodels>=0.14; sys_platform == 'win32'",
     "statsmodels>=0.14; sys_platform == 'linux'",
-    "seaborn==0.13; sys_platform == 'darwin'",
+    "scipy>=1.16; sys_platform == 'darwin'",
+    "scipy>=1.16; sys_platform == 'win32'",
+    "scipy>=1.16; sys_platform == 'linux'",
+    "seaborn>=0.13; sys_platform == 'darwin'",
     "seaborn>=0.13; sys_platform == 'win32'",
     "seaborn>=0.13; sys_platform == 'linux'",
-    "matplotlib==3.11; sys_platform == 'darwin'",
+    "matplotlib>=3.11; sys_platform == 'darwin'",
     "matplotlib>=3.11; sys_platform == 'win32'",
     "matplotlib>=3.11; sys_platform == 'linux'",
 ]