TRENDY method code files by Yue Wang (20581715)

“…<p dir="ltr">code files for TRENDY method, used for inferring gene regulatory networks (GRN) from single-cell gene expression data</p><p dir="ltr">TRENDY algorithm itself uses the following packages: numpy=1.24.3, scipy=1.13.1, sklearn=1.4.2, torch=2.2.2,</p><p dir="ltr">other algorithms and comparison files need extra packages: pingouin=0.5.3, pandas=2.2.2, xgboost=2.0.3</p><p dir="ltr">warning: the NonlinearODEs algorithm (xgbgrn.py) runs well on Windows, but might crash on MacOS</p><p dir="ltr">manuscript for TRENDY method: GRN_transformer.pdf</p><p dir="ltr">major code files:</p><p dir="ltr">TRENDY_tutorial.py: a tutorial for using TRENDY method. to apply the TRENDY method, it also needs the following files: models.py, wendy_solver.py in previous_methods folder, trendy_1.pth and trendy_2.pth in weights folder</p><p dir="ltr">models.py: contains all three versions of the TE(k) model</p><p dir="ltr">train_trendy_first_half.py: train the TE(k=1) model for the first half of TRENDY method. the trained weights trendy_1.pth is in the folder weights</p><p dir="ltr">train_trendy_second_half.py: train the TE(k=3) model for the second half of TRENDY method. the trained weights trendy_2.pth is in the folder weights</p><p dir="ltr">code files for training other models:</p><p dir="ltr">train_GENIE3_rev.py: train the GENIE3_rev method. the trained weights genie_rev.pth is in the folder weights</p><p dir="ltr">train_NonlinearODEs_rev.py: train the NonlinearODEs_rev method. the trained weights nlode_rev.pth is in the folder weights</p><p dir="ltr">train_SINCERITIES_rev.py: train the SINCERITIES_rev method. the trained weights sinc_rev.pth is in the folder weights</p><p dir="ltr">code files for comparing different methods:</p><p dir="ltr">test_SINC_new.py: used to compare different methods on SINC data</p><p dir="ltr">test_DREAM4_new.py: used to compare different methods on DREAM4 data</p><p dir="ltr">test_THP1_new.py: used to compare different methods on THP-1 data</p><p dir="ltr">test_hESC_new.py: used to compare different methods on hESC data</p><p dir="ltr">code for previously known methods, all in the folder previous_methods:</p><p dir="ltr">sincerities.py: code for SINCERITIES method</p><p dir="ltr">xgbgrn.py: code for NonlinearODEs method</p><p dir="ltr">GENIE3.py: code for GENIE3 method</p><p dir="ltr">wendy_solver.py: code for WENDY method</p><p dir="ltr">auxiliary code files:</p><p dir="ltr">methods.py: contains functions for different methods</p><p dir="ltr">evaluation.py: compare the inferred GRN with the ground truth GRN and calculate AUROC and AUPRC</p><p dir="ltr">plots_new.py: draw plots</p><p dir="ltr">nd_alg.py: code for network deconvolution method for enhancing inferred GRNs</p><p dir="ltr">brane_alg.py: code for BRANE Cut method for enhancing inferred GRNs</p><p dir="ltr">generate training data, all in the folder Data_generation:</p><p dir="ltr">A_data_generation.py generates a random GRN, generate.py generates all files in the following folder total_data_10, the other four files are previously known methods</p><p dir="ltr">data sets:</p><p dir="ltr">folder total_data_10 (<a href="https://zenodo.org/records/13929908" rel="nofollow" target="_blank">https://zenodo.org/records/13929908</a>, not uploaded here): saves the generated data for training and validation. for different endings: A is the ground truth GRN, cov is the covariance matrix, data is the original data, genie is the inferred GRN by GENIE3, nlode is the inferred GRN by NonlinearODEs, revcov is the Ktstar matrix, sinc is the inferred GRN by SINCERITIES, wendy is the inferred GRN by WENDY. these data files are generated by the files in folder Data_generation. here we only upload the files for testing. for full files of this folder, see <a href="https://zenodo.org/records/13929908" rel="nofollow" target="_blank">https://zenodo.org/records/13929908</a></p><p dir="ltr">folder rev_wendy_all_10 (not uploaded here. see <a href="https://zenodo.org/records/13929908" rel="nofollow" target="_blank">https://zenodo.org/records/13929908</a>): saves the inferred Kt' matrix (xxx_ktstar files) and A_1 matrix (xxx_revwendy files) in TRENDY</p><p dir="ltr">folder SINC: ground truth GRNs and inferred GRNs in SINC data set. …”

Table1_Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy... by Shule Jiang (20295756)

“…Pearson correlation analysis was then utilized to select genes linked to mitochondrial function and PCD (M-PCD). …”

Table2_Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy... by Shule Jiang (20295756)

“…Pearson correlation analysis was then utilized to select genes linked to mitochondrial function and PCD (M-PCD). …”

Table3_Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy... by Shule Jiang (20295756)

“…Pearson correlation analysis was then utilized to select genes linked to mitochondrial function and PCD (M-PCD). …”

Table4_Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy... by Shule Jiang (20295756)

“…Pearson correlation analysis was then utilized to select genes linked to mitochondrial function and PCD (M-PCD). …”

Image1_Transcriptome combined with Mendelian randomization to screen key genes associated with mitochondrial and programmed cell death causally associated with diabetic retinopathy... by Shule Jiang (20295756)

“…Pearson correlation analysis was then utilized to select genes linked to mitochondrial function and PCD (M-PCD). …”

Data_Sheet_3_Potential diagnostic markers and therapeutic targets for non-alcoholic fatty liver disease and ulcerative colitis based on bioinformatics analysis and machine learning... by Zheng Luo (284622)

“…Additionally, we used the CIBERSORT algorithm to explore immune infiltration patterns in both NAFLD and UC samples. …”

Data_Sheet_4_Potential diagnostic markers and therapeutic targets for non-alcoholic fatty liver disease and ulcerative colitis based on bioinformatics analysis and machine learning... by Zheng Luo (284622)

“…Additionally, we used the CIBERSORT algorithm to explore immune infiltration patterns in both NAFLD and UC samples. …”

Data_Sheet_2_Potential diagnostic markers and therapeutic targets for non-alcoholic fatty liver disease and ulcerative colitis based on bioinformatics analysis and machine learning... by Zheng Luo (284622)

“…Additionally, we used the CIBERSORT algorithm to explore immune infiltration patterns in both NAFLD and UC samples. …”

Data_Sheet_1_Potential diagnostic markers and therapeutic targets for non-alcoholic fatty liver disease and ulcerative colitis based on bioinformatics analysis and machine learning... by Zheng Luo (284622)

“…Additionally, we used the CIBERSORT algorithm to explore immune infiltration patterns in both NAFLD and UC samples. …”

PR curves of improved YOLOv5s. by Tianyu Cheng (5075000)

“…Experimental results show that the mAP@0.5% of improved YOLOv5s algorithm increases from 92.7% to 99.3%, which means 6.6% accuracy improvement compared with the YOLOv5s model. …”

The improved DeepSORT framework. by Tianyu Cheng (5075000)

“…Experimental results show that the mAP@0.5% of improved YOLOv5s algorithm increases from 92.7% to 99.3%, which means 6.6% accuracy improvement compared with the YOLOv5s model. …”

YOLOv5s model with attention modules. by Tianyu Cheng (5075000)

“…Experimental results show that the mAP@0.5% of improved YOLOv5s algorithm increases from 92.7% to 99.3%, which means 6.6% accuracy improvement compared with the YOLOv5s model. …”

Table 12_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.xlsx by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”

Table 9_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.xlsx by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”

Table 8_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.xlsx by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”

Table 1_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.xlsx by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”

Table 2_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.xlsx by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”

Table 3_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.xlsx by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”

Table 5_Decoding immune-metabolic crosstalk in ARDS: a transcriptomic exploration of biomarkers, cellular dynamics, and therapeutic pathways.doc by Ting Wu (106368)

“…RT-qPCR confirmed a significant upregulation of SMARCD3 and TCN1 in ARDS samples, aligning with dataset expression analysis results. Both in vitro and in vivo experiments demonstrated that modulation of SMARCD3 and TCN1 (but not RPL14) significantly affected mitochondrial function, oxidative stress, apoptosis, glucose metabolism and inflammatory cytokine expression.…”