Volcano for CLK1 high vs low Exon 4 HGG samples #8
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naqvia
changed the title
Merged
jharenza
reviewed
Jan 14, 2025
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| SRSF_targets <- c("BIN1", "RON", "BCL2L1", "MKNK2", "CASP9", | ||
| "CD45", "BCL2L1", "TP53", "FAS", "MCL1", | ||
| "TPM1", "SYN1", "TAU", "ERBB2", "SMN2", | ||
| "FAS", "MYC", "VEGF", "MCL1", "CASP2", | ||
| "FN1", "DMD", "CD44", "CASP8", "KLF6") | ||
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do you have a source for these?
jharenza
reviewed
Jan 14, 2025
| rmats_full_file = file.path(data_dir, "splice-events-rmats.tsv.gz") | ||
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| rmats_full_df <- vroom(rmats_full_file) | ||
| rmats_se_full_df <- vroom("~/d3b_coding/neoepitope-identification/data/pbta-splice-events-rmats.SE.tsv.gz") |
jharenza
reviewed
Jan 14, 2025
| @@ -56,6 +56,7 @@ depmap_glioma <- depmap_data %>% | |||
| depmap_data_KNS42 <- depmap_glioma %>% | |||
| filter(`Cell line` =="KNS42") | |||
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I don't think this script should be changed in this PR?
jharenza
reviewed
Jan 14, 2025
| @@ -0,0 +1,97 @@ | |||
| # Libraries | |||
| suppressPackageStartupMessages({ | |||
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I think you may need a merge with main, as you have some scripts and modules updating here which should not be
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something weird is going on. Lets review and merge the previous PR #7 first and will re-do this one. It should only be one script. |
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Volcano and ORA for CLK1 high vs low exon 4 (significantly/differential). TNFA signaling via nFkB is still the most enriched in down-regulated genes.