<commit_before># DE_tools
DE analysis function for edgeR, DESeq2, and Limma-Voom.

##How To Use It

Rscript DE_analysis.R /fullpathTo/rawCount.txt /fullpathTo/metatable.txt Control KO /fullpathTo/DEG_analysis_res/ 2 3 True True /fullpathTo/DE-Analysis-AllComb-Fn.R 0.05 1.5 > /fullpathTo/DE_analysis.Rout.log 2> /fullpathTo/DE_analysis.Rerr.log

Where, the following parameters are:

1. raw count input: /fullpathTo/rawCount.txt

2. metadata table input: /fullpathTo/metatable.txt

3. group 1 name: e.g. Control, consistent with metatable.txt group information

4. group 2 name: e.g. KO, consistent with metatable.txt group information

5. output directory: /fullpathTo/outputDir

6. group cutoff: 2

7. cpm cutoff: 3

8. logical, whether to save the results: True

9. logical, whether to use orignal p-value or FDR corrected p-value for DEGs identification: True

10. full path to the source code: /fullpathTo/DE-Analysis-AllComb-Fn.R

The log output - DE_analysis.Rout.log include the results summary, and log output DE_analysis.Rerr.log includes the error message if program runs incorrectly.<commit_msg>update readme for visualization<commit_after># DE_tools
DE analysis function for edgeR, DESeq2, and Limma-Voom.

##How To Use It

###To run DE_analysis.R

Rscript DE_analysis.R /fullpathTo/rawCount.txt /fullpathTo/metatable.txt Control KO /fullpathTo/DEG_analysis_res/ 2 3 True True /fullpathTo/DE-Analysis-AllComb-Fn.R 0.05 1.5 > /fullpathTo/DE_analysis.Rout.log 2> /fullpathTo/DE_analysis.Rerr.log

Where, the following parameters are:

1. raw count input: /fullpathTo/rawCount.txt

2. metadata table input: /fullpathTo/metatable.txt

3. group 1 name: e.g. Control, consistent with metatable.txt group information

4. group 2 name: e.g. KO, consistent with metatable.txt group information

5. output directory: /fullpathTo/outputDir

6. group cutoff: 2

7. cpm cutoff: 3

8. logical, whether to save the results: True

9. logical, whether to use orignal p-value or FDR corrected p-value for DEGs identification: True

10. full path to the source code: /fullpathTo/DE-Analysis-AllComb-Fn.R

11. p-values / FRD adjusted p-value: 0.05

12. FC(Fold Change) cutoff: 1.5

The log output - DE_analysis.Rout.log include the results summary, and log output DE_analysis.Rerr.log includes the error message if program runs incorrectly.

###To run DE_analysis_visualization.R

Rscript DE_analysis_visualization.R /fullpathTo/DE_analysis_vis_Fn.R /fullpathTo/DEG_analysis_res group1 group2 2 3 0.05 1.5

Where, the following parameters are:

1. function code: /fullpathTo/DE_analysis_vis_Fn.R

2. DE analysis results directory in above running: /fullpathTo/DEG_analysis_res

3. group 1 name: e.g. Control, consistent with above running 

4. group 2 name: e.g. KO, consistent with above running 

5. group cutoff: 2

6. cpm cutoff: 3

7. p-values / FRD adjusted p-value: 0.05

8. FC(Fold Change) cutoff: 1.5





{'fraction_non_alphanumeric': 0.08565531475748193, 'fraction_numerical': 0.028551771585827314, 'mean_word_length': 4.066202090592334, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3153624', 'n_tokens_mistral': 1028, 'n_tokens_neox': 954, 'n_words': 348}