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Kris Alavattam

Removing rough-draft results files

Nov 29, 2023

c0111b1 · Nov 29, 2023

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Name		Name	Last commit message	Last commit date
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notebook		notebook	Removing rough-draft results files	Nov 29, 2023
README.md		README.md	First of what will amount to be a lot reorganization, etc. in prep fo…	Jul 27, 2023
collate_sea-tsv.sh		collate_sea-tsv.sh	See time_FHCC.xlsx for 2023-0613 and 2023-0614	Jun 15, 2023
rough-draft_calculate-fold-change_mean-TPM_WT-G1-SS-vs-WT-Q-SS.no-log2.R		rough-draft_calculate-fold-change_mean-TPM_WT-G1-SS-vs-WT-Q-SS.no-log2.R	2023-0913: Get to rough stopping place with calculation of fold-chang…	Sep 13, 2023
rough-draft_calculate-fold-change_mean-TPM_WT-G1-SS-vs-WT-Q-SS.scraps.R		rough-draft_calculate-fold-change_mean-TPM_WT-G1-SS-vs-WT-Q-SS.scraps.R	2023-0913: Get to rough stopping place with calculation of fold-chang…	Sep 13, 2023
rough-draft_calculate-fold-change_mean-TPM_WT-G1-SS-vs-WT-Q-SS.yes-log2.R		rough-draft_calculate-fold-change_mean-TPM_WT-G1-SS-vs-WT-Q-SS.yes-log2.R	2023-0913: Get to rough stopping place with calculation of fold-chang…	Sep 13, 2023
rough-draft_coverage-tracks.sh		rough-draft_coverage-tracks.sh	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_coverage-tracks_timecourse_size-effect.sh		rough-draft_coverage-tracks_timecourse_size-effect.sh	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_draw_scatter-plots.R		rough-draft_draw_scatter-plots.R	Did work to conclude the bioinformatics to-do items described in the …	Sep 26, 2023
rough-draft_estimate-RNA-degredation.R		rough-draft_estimate-RNA-degredation.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_evaluate-categories_expression.R		rough-draft_evaluate-categories_expression.R	Small updates to code to print out tables associated with Fig. 1A	Oct 25, 2023
rough-draft_evaluate-categories_expression_initial.Rmd		rough-draft_evaluate-categories_expression_initial.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_evaluate-categories_expression_scraps_initial.Rmd		rough-draft_evaluate-categories_expression_scraps_initial.Rmd	Numerous updates to files in repo directory 2023-0215/ as I regenerat…	May 23, 2023
rough-draft_handle-matrices-gtfs.R		rough-draft_handle-matrices-gtfs.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_handle-tables_establish-study-design.R		rough-draft_handle-tables_establish-study-design.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_new-approach-to-analyses.R		rough-draft_new-approach-to-analyses.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_new-approach-to-analyses_tests-scraps.R		rough-draft_new-approach-to-analyses_tests-scraps.R	See time_FHCC.xlsx entry for 2023-0606	Jun 6, 2023
rough-draft_plot-TPM_N-varies-on-SS.scraps.R		rough-draft_plot-TPM_N-varies-on-SS.scraps.R	See time_FHCC.xlsx for 2023-0630	Jul 1, 2023
rough-draft_plot-TPM_N-varies-on-SS_LFC-varies-on-TPM.R		rough-draft_plot-TPM_N-varies-on-SS_LFC-varies-on-TPM.R	Did work to conclude the bioinformatics to-do items described in the …	Sep 26, 2023
rough-draft_plot-distributions_expression.R		rough-draft_plot-distributions_expression.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_plot-distributions_length.R		rough-draft_plot-distributions_length.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_run-analyses_Fig-5B-5C.R		rough-draft_run-analyses_Fig-5B-5C.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_run-analyses_GO.R		rough-draft_run-analyses_GO.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_run-analyses_rlog-PCA_write-rds.R		rough-draft_run-analyses_rlog-PCA_write-rds.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_run-analyses_rlog-PCA_write-rds.notes-2.txt		rough-draft_run-analyses_rlog-PCA_write-rds.notes-2.txt	Continuing to complete to-do tasks for the RRP6-NAB3 manuscript; see …	Jul 4, 2023
rough-draft_run-analyses_rlog-PCA_write-rds.notes.txt		rough-draft_run-analyses_rlog-PCA_write-rds.notes.txt	Continuing to complete to-do tasks for the RRP6-NAB3 manuscript; see …	Jul 4, 2023
rough-draft_run-analyses_rlog-PCA_write-rds.scraps.R		rough-draft_run-analyses_rlog-PCA_write-rds.scraps.R	Continuing to complete to-do tasks for the RRP6-NAB3 manuscript; see …	Jul 4, 2023
rough-draft_timecourse-samples_processing_part-1a.R		rough-draft_timecourse-samples_processing_part-1a.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_timecourse-samples_processing_part-1b.R		rough-draft_timecourse-samples_processing_part-1b.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_timecourse-samples_processing_part-1c.R		rough-draft_timecourse-samples_processing_part-1c.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
rough-draft_timecourse-samples_processing_part-2a.R		rough-draft_timecourse-samples_processing_part-2a.R	Moving forward with the rlog/PCA work; in referencing old code, clean…	Jun 19, 2023
rough-draft_write-gtf-blacklist.R		rough-draft_write-gtf-blacklist.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
run_chi-sq_quantile-filtered-coding-assignments.R		run_chi-sq_quantile-filtered-coding-assignments.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
test_count_features.md		test_count_features.md	Work for 2023-0226: Reading in and munging featureCounts, then realiz…	Feb 27, 2023
tutorial_collapse-intersecting-regions.R		tutorial_collapse-intersecting-regions.R	Continued work for making the 'representative coding/noncoding/etc' g…	Apr 27, 2023
tutorial_extract-non-overlapping-regions.R		tutorial_extract-non-overlapping-regions.R	Pushing code that I forgot to push sooner	May 2, 2023
work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-0.Rmd		work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-0.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-1.Rmd		work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-1.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-2.R		work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-2.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-2_legend.txt		work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-2_legend.txt	Pushing updates to 'work_assess-process_R64-1-1-gff3_categorize-Trini…	Jun 17, 2023
work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-3.R		work_assess-process_R64-1-1-gff3_categorize-Trinity-transfrags_part-3.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assessment-processing_gtfs_part-0.5_non-Trinity.Rmd		work_assessment-processing_gtfs_part-0.5_non-Trinity.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assessment-processing_gtfs_part-0_Trinity-etc.md		work_assessment-processing_gtfs_part-0_Trinity-etc.md	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assessment-processing_gtfs_part-1.5_Trinity.R		work_assessment-processing_gtfs_part-1.5_Trinity.R	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assessment-processing_gtfs_part-1_Trinity.Rmd		work_assessment-processing_gtfs_part-1_Trinity.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_assessment-processing_gtfs_part-2_Trinity.md		work_assessment-processing_gtfs_part-2_Trinity.md	See time_FHCC.xlsx for 2023-0617	Jun 17, 2023
work_calculate_uni-multimappers-etc.md		work_calculate_uni-multimappers-etc.md	See time_FHCC.xlsx entry for 2023-0609; also, in solving the naming p…	Jun 10, 2023
work_combine-gtfs_processed-ncRNA_part-0.Rmd		work_combine-gtfs_processed-ncRNA_part-0.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_combine-gtfs_processed-ncRNA_part-1.md		work_combine-gtfs_processed-ncRNA_part-1.md	See time_FHCC.xlsx entry for 2023-0608, plus pushing some code from b…	Jun 8, 2023
work_combine-gtfs_processed-non-pa-ncRNA_part-0.Rmd		work_combine-gtfs_processed-non-pa-ncRNA_part-0.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_combine-gtfs_processed-non-pa-ncRNA_part-1.md		work_combine-gtfs_processed-non-pa-ncRNA_part-1.md	Moving forward with the rlog/PCA work; in referencing old code, clean…	Jun 19, 2023
work_combine-gtfs_processed-pa-ncRNA_part-0.Rmd		work_combine-gtfs_processed-pa-ncRNA_part-0.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_combine-gtfs_processed-pa-ncRNA_part-1.md		work_combine-gtfs_processed-pa-ncRNA_part-1.md	See time_FHCC.xlsx for 2023-0617	Jun 17, 2023
work_count-features_assessed-processed-R64-1-1-gff3s.md		work_count-features_assessed-processed-R64-1-1-gff3s.md	Continued work to complete the combined processed/pa-ncRNA gtf and co…	May 24, 2023
work_count_features_featureCounts.md		work_count_features_featureCounts.md	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_count_features_htseq-count.md		work_count_features_htseq-count.md	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_env-building.md		work_env-building.md	Continued work on gtf/gff3-related things	Apr 20, 2023
work_evaluation-etc_rough-draft_Rrp6-WT_SS_timecourse_groupwise.Rmd		work_evaluation-etc_rough-draft_Rrp6-WT_SS_timecourse_groupwise.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_evaluation-etc_variables_pairwise-groupwise.Rmd		work_evaluation-etc_variables_pairwise-groupwise.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_evaluation-etc_variables_pairwise-groupwise.TODOs-scraps-etc.txt		work_evaluation-etc_variables_pairwise-groupwise.TODOs-scraps-etc.txt	Cleaning up 2022_transcriptome-construction, pushing code in the mids…	Mar 27, 2023
work_evaluation-etc_variables_pairwise-groupwise.tmp-gw.R		work_evaluation-etc_variables_pairwise-groupwise.tmp-gw.R	Work for 2023-0403: Working on code related to bigwig-generation, cal…	Apr 3, 2023
work_evaluation-etc_variables_pairwise-groupwise.tmp-pw.R		work_evaluation-etc_variables_pairwise-groupwise.tmp-pw.R	Work for 2023-0403: Working on code related to bigwig-generation, cal…	Apr 3, 2023
work_examine-snRNA-snoRNA-annotations_part-1.Rmd		work_examine-snRNA-snoRNA-annotations_part-1.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_examine-snRNA-snoRNA-annotations_part-2.md		work_examine-snRNA-snoRNA-annotations_part-2.md	Numerous updates to files in repo directory 2023-0215/ as I regenerat…	May 23, 2023
work_gff3_convert-strand-designations.Rmd		work_gff3_convert-strand-designations.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_gff3_include-20S.md		work_gff3_include-20S.md	Work, early morning/morning of 2023-0331: Calling htseq-count with al…	Mar 31, 2023
work_make-blacklist-etc.py		work_make-blacklist-etc.py	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_model-variables.md		work_model-variables.md	See time_FHCC.xlsx entry for 2023-0609; also, in solving the naming p…	Jun 10, 2023
work_normalization-etc_rough-draft_NNS_vary-on-transcription.Rmd		work_normalization-etc_rough-draft_NNS_vary-on-transcription.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_normalization-etc_rough-draft_OsTIR-NNS_vary-on-strain.Rmd		work_normalization-etc_rough-draft_OsTIR-NNS_vary-on-strain.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_normalization-etc_rough-draft_wild-type_vary-on-state.Rmd		work_normalization-etc_rough-draft_wild-type_vary-on-state.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_normalization-etc_rough-draft_wild-type_vary-on-state_antisense.Rmd		work_normalization-etc_rough-draft_wild-type_vary-on-state_antisense.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_prepare-data_GEO.md		work_prepare-data_GEO.md	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_prepare-data_GEO_matrices.R		work_prepare-data_GEO_matrices.R	Work, Saturday and Sunday: Working up the code for estimating relativ…	Sep 10, 2023
work_preprocess-prepare_htseq-counts-matrices_gtf-gff3_etc.Rmd		work_preprocess-prepare_htseq-counts-matrices_gtf-gff3_etc.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_representative-non-coding-transcriptome_part-0.md		work_representative-non-coding-transcriptome_part-0.md	Fixing merge (choosing work performed on MacBook over the last few days)	Jul 27, 2023
work_representative-non-coding-transcriptome_part-1.md		work_representative-non-coding-transcriptome_part-1.md	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_representative-non-coding-transcriptome_part-2.Rmd		work_representative-non-coding-transcriptome_part-2.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_representative-non-coding-transcriptome_part-3.md		work_representative-non-coding-transcriptome_part-3.md	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_representative-non-coding-transcriptome_part-4.Rmd		work_representative-non-coding-transcriptome_part-4.Rmd	End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …	Sep 9, 2023
work_representative-non-coding-transcriptome_part-5.md		work_representative-non-coding-transcriptome_part-5.md	See time_FHCC.xlsx entry for 2023-0609; also, in solving the naming p…	Jun 10, 2023
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