{"id":18880200,"url":"https://github.com/genepattern/combat_seq","last_synced_at":"2026-02-20T12:30:16.662Z","repository":{"id":40735767,"uuid":"507989458","full_name":"genepattern/ComBat_Seq","owner":"genepattern","description":"Batch effect adjustment based on negative binomial regression for RNA sequencing count data. 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Improved model based on ComBat. \u003cbr\u003e\r\n#### Parameters\r\nTo run ComBat Seq, these inputs are used: \r\n  1. **input matrix (required)**\r\n      - The input matrix is a counts matrix with dimensions gene x sample. The input counts matrix. Can be a .GCT or a .tsv (tab separated value) file. Rows should be genes, column should be samples, and the value are counts. File format documentation for GCT files: https://www.genepattern.org/file-formats-guide Some sample inputs can be found here: https://github.com/genepattern/ComBat_Seq/tree/develop/data\r\n      - The input matrix should have corresponding sample names for the first row, and corresponding genes for the first column. \u003cbr\u003e \r\n\r\n##### Example input matrix:\r\n| Name      | Sample 1 Name | Sample 2 Name | Sample 3 Name | Sample 4 Name | Sample 5 Name | ... | Sample m Name |\r\n| ----------- | ----------- | ----------- | ----------- | ----------- | ----------- | ----------- |  ----------- | \r\n| Gene 1 Name     | 30       | 49       | 554       | 394      | 345     |  ... | 33|\r\n| Gene 2 Name  | 839        | 485        | 123        | 223        | 339        |  ... | 234 |\r\n| ... | ... | ... | ... | ... | ... | ... | ... |\r\n| Gene n Name | 423 | 442 | 123 | 553 | 754 | ... | 22|\r\n\r\n  2. **batch information (required)**\r\n      - Batch information contain information on batches. It is a table that looks like the following:\r\n      - The file can be a .CLS file contaning only batch information, or a .tsv (tab separated file) containing batch, group, and any other additional information as long as it follows the format below. \u003cbr\u003e\r\n\r\n##### Example batch information file\r\n| Samples      | Sample 1 Name | Sample 2 Name | Sample 3 Name | Sample 4 Name | Sample 5 Name | ... | Sample m Name\r\n| ----------- | ----------- | ----------- | ----------- | ----------- | ----------- | ----------- | ----------- |\r\n| Batch      | 1       | 1       | 2       | 2      | 2     |  ... | 4 |\r\n| Group   | Group 1 info        | Group 1 info        | Group 1 info        | Group 1 info        | Group 1 info        |  ... | Group 3 info |\r\n| ... | ... | ... | ... | ... | ... | ... | ... | \r\n\u003cbr\u003e\r\n\u003cbr\u003e \r\n      \r\n  3. covariates (optional)\r\n      - Row names for covariates to use for this run of ComBat Seq. \r\n  4. **output prefix (required)**\r\n      - Prefix for output filenames. \r\n#### Advanced Parameters\r\n  5. Shrink\r\n      - Whether to apply empirical Bayes estimation on dispersion.\r\n  6. gene subset n\r\n      - Number of genes to use in empirical Bayes estimation, only useful when shrink = Yes\r\n  7. covariance matrix\r\n      - If you wish to specify multiple biological variables. Model matrix for other covariates to include in the linear model besides batch and condition of interest.\r\n\r\n## Documentation\r\n  - ComBat-Seq author: Yuqing Zhang. Original GitHub Repo: https://github.com/zhangyuqing/ComBat-seq\r\n  - Docker image used: genepattern/combat_seq:v1\r\n\r\n\r\n\r\n## Citation\r\nYuqing Zhang, Giovanni Parmigiani, W Evan Johnson, ComBat-seq: batch effect adjustment for RNA-seq count data, NAR Genomics and Bioinformatics, Volume 2, Issue 3, 1 September 2020, lqaa078, https://doi.org/10.1093/nargab/lqaa078\r\n\r\n\r\n## Contact\r\n  - Edwin Huang: edh021@cloud.ucsd.edu\r\n\r\n\r\n\r\n\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenepattern%2Fcombat_seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenepattern%2Fcombat_seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenepattern%2Fcombat_seq/lists"}