Merge pull request #75 from broadinstitute/cleanup

Cleanup
broadinstitute · Jan 24, 2023 · e28385d · e28385d
2 parents 6c3e2cc + bb40908
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diff --git a/config_files/README.md → ...ile-cell-lines-new/config_files/README.md b/config_files/README.md → ...ile-cell-lines-new/config_files/README.md
diff --git a/config_files/config_batch8.yml → ...-lines-new/config_files/config_batch8.yml b/config_files/config_batch8.yml → ...-lines-new/config_files/config_batch8.yml
diff --git a/...h8_normalized_feature_select_batch.csv.gz → ...h8_normalized_feature_select_batch.csv.gz b/...h8_normalized_feature_select_batch.csv.gz → ...h8_normalized_feature_select_batch.csv.gz
diff --git a/...atch8_normalized_feature_select_batch.gct → ...atch8_normalized_feature_select_batch.gct b/...atch8_normalized_feature_select_batch.gct → ...atch8_normalized_feature_select_batch.gct
diff --git a/gct/2022_09_07_Batch8/Batch8_NoCostes.gct → ...gct/2022_09_07_Batch8/Batch8_NoCostes.gct b/gct/2022_09_07_Batch8/Batch8_NoCostes.gct → ...gct/2022_09_07_Batch8/Batch8_NoCostes.gct
diff --git a/...un_normalized_feature_select_batch.csv.gz → ...un_normalized_feature_select_batch.csv.gz b/...un_normalized_feature_select_batch.csv.gz → ...un_normalized_feature_select_batch.csv.gz
diff --git a/...Rerun_normalized_feature_select_batch.gct → ...Rerun_normalized_feature_select_batch.gct b/...Rerun_normalized_feature_select_batch.gct → ...Rerun_normalized_feature_select_batch.gct
diff --git a/...9_22_Batch8Rerun/Batch8Rerun_NoCostes.gct → ...9_22_Batch8Rerun/Batch8Rerun_NoCostes.gct b/...9_22_Batch8Rerun/Batch8Rerun_NoCostes.gct → ...9_22_Batch8Rerun/Batch8Rerun_NoCostes.gct
diff --git a/gct/README.md → 2.profile-cell-lines-new/gct/README.md b/gct/README.md → 2.profile-cell-lines-new/gct/README.md
diff --git a/...RISPRi_plate1/cmQTL_CRISPRi_plate1.csv.gz → ...RISPRi_plate1/cmQTL_CRISPRi_plate1.csv.gz b/...RISPRi_plate1/cmQTL_CRISPRi_plate1.csv.gz → ...RISPRi_plate1/cmQTL_CRISPRi_plate1.csv.gz
diff --git a/...te1/cmQTL_CRISPRi_plate1_augmented.csv.gz → ...te1/cmQTL_CRISPRi_plate1_augmented.csv.gz b/...te1/cmQTL_CRISPRi_plate1_augmented.csv.gz → ...te1/cmQTL_CRISPRi_plate1_augmented.csv.gz
diff --git a/...e1/cmQTL_CRISPRi_plate1_normalized.csv.gz → ...e1/cmQTL_CRISPRi_plate1_normalized.csv.gz b/...e1/cmQTL_CRISPRi_plate1_normalized.csv.gz → ...e1/cmQTL_CRISPRi_plate1_normalized.csv.gz
diff --git a/...e1_normalized_feature_select_batch.csv.gz → ...e1_normalized_feature_select_batch.csv.gz b/...e1_normalized_feature_select_batch.csv.gz → ...e1_normalized_feature_select_batch.csv.gz
diff --git a/...T_rerun_20220919/MT_rerun_20220919.csv.gz → ...T_rerun_20220919/MT_rerun_20220919.csv.gz b/...T_rerun_20220919/MT_rerun_20220919.csv.gz → ...T_rerun_20220919/MT_rerun_20220919.csv.gz
diff --git a/...220919/MT_rerun_20220919_augmented.csv.gz → ...220919/MT_rerun_20220919_augmented.csv.gz b/...220919/MT_rerun_20220919_augmented.csv.gz → ...220919/MT_rerun_20220919_augmented.csv.gz
diff --git a/...20919/MT_rerun_20220919_normalized.csv.gz → ...20919/MT_rerun_20220919_normalized.csv.gz b/...20919/MT_rerun_20220919_normalized.csv.gz → ...20919/MT_rerun_20220919_normalized.csv.gz
diff --git a/...19_normalized_feature_select_batch.csv.gz → ...19_normalized_feature_select_batch.csv.gz b/...19_normalized_feature_select_batch.csv.gz → ...19_normalized_feature_select_batch.csv.gz
diff --git a/profiles/README.md → 2.profile-cell-lines-new/profiles/README.md b/profiles/README.md → 2.profile-cell-lines-new/profiles/README.md
diff --git a/01_MakePhenoCov.R → 3.cmqtl/01_MakePhenoCov.R b/01_MakePhenoCov.R → 3.cmqtl/01_MakePhenoCov.R
diff --git a/02_RunAssociation.sh → 3.cmqtl/02_RunAssociation.sh b/02_RunAssociation.sh → 3.cmqtl/02_RunAssociation.sh
diff --git a/03_GetLambda_QQ.R → 3.cmqtl/03_GetLambda_QQ.R b/03_GetLambda_QQ.R → 3.cmqtl/03_GetLambda_QQ.R
diff --git a/03_Run.sh → 3.cmqtl/03_Run.sh b/03_Run.sh → 3.cmqtl/03_Run.sh
diff --git a/04_GetdataForManhattanPlot.R → 3.cmqtl/04_GetdataForManhattanPlot.R b/04_GetdataForManhattanPlot.R → 3.cmqtl/04_GetdataForManhattanPlot.R
diff --git a/04_Run.sh → 3.cmqtl/04_Run.sh b/04_Run.sh → 3.cmqtl/04_Run.sh
diff --git a/05_ManhattanPlot.R → 3.cmqtl/05_ManhattanPlot.R b/05_ManhattanPlot.R → 3.cmqtl/05_ManhattanPlot.R
diff --git a/06_PapersTable.R → 3.cmqtl/06_PapersTable.R b/06_PapersTable.R → 3.cmqtl/06_PapersTable.R
diff --git a/cmqtl_onErisone_current.r → 3.cmqtl/cmqtl_onErisone_current.r b/cmqtl_onErisone_current.r → 3.cmqtl/cmqtl_onErisone_current.r
diff --git a/README.md b/README.md
@@ -1,19 +1,6 @@
 # Cell Morphology Quantitative Trait Loci (cmQTL)
 
-Defining the genetic architecture of cell morphology
-
-## Data
-
-We are collecting cell painting data from induced pluripotent stem cells (iPSC) derived from ~1,000 patients.
-We also have matched genotype data from these patients.
-Our goal is to determine if specific genotypes can be mapped to cell morphology.
-
-## Determining Cell Culture Conditions
-
-Our first step is to determine optimal conditions at which to plate samples in order to generate morphological profiles.
-We describe our approach in [0.pilot-determine-conditions](0.pilot-determine-conditions/).
-
-Based on these analyses, we determined that the optimal conditions included plating cells for 6 hours at 10,000 plate density.
+High-dimensional phenotyping to define the genetic basis of cellular morphology
 
 ## Reproducibility
 

diff --git a/archive/README.md → _archive/README.md b/archive/README.md → _archive/README.md
diff --git a/archive/analysis.Rmd → _archive/analysis.Rmd b/archive/analysis.Rmd → _archive/analysis.Rmd
diff --git a/archive/analysis.sh → _archive/analysis.sh b/archive/analysis.sh → _archive/analysis.sh
diff --git a/archive/annotate_script.R → _archive/annotate_script.R b/archive/annotate_script.R → _archive/annotate_script.R
diff --git a/archive/select_images_to_print.Rmd → _archive/select_images_to_print.Rmd b/archive/select_images_to_print.Rmd → _archive/select_images_to_print.Rmd
diff --git a/audit/README.md b/audit/README.md
diff --git a/batchfiles/README.md b/batchfiles/README.md
diff --git a/log/README.md b/log/README.md
diff --git a/pipelines/README.md b/pipelines/README.md
diff --git a/quality_control/README.md b/quality_control/README.md
diff --git a/single_cell/README.md b/single_cell/README.md