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Revision Author Date Message Commit Date
e25f3d9 Update LICENSE 17 December 2020, 00:02:59 UTC
3c2f81d Update README.md 16 December 2020, 23:59:00 UTC
ffcc48a Create LICENSE 16 December 2020, 15:55:15 UTC
dafa6cf added additional genes manually to beeswarm plot script 27 October 2020, 19:24:11 UTC
5070c64 added color to the plot showing how c values change for the same gene from low to med to high dose 11 October 2020, 22:26:56 UTC
17d4c33 minor changes to mean/variance plot height when saving plots as svg 07 October 2020, 21:46:08 UTC
47080de updated mean/variance plots for poisson distribution assumption and changed height of p value by bin composite plots 07 October 2020, 16:46:16 UTC
e356f32 added new x tick locations to p value plots 06 October 2020, 19:40:10 UTC
e1f822d updated x axis ticks and standardized x axis limits 06 October 2020, 18:53:13 UTC
02787df lengthened a composite plot to 5 columns 06 October 2020, 17:21:32 UTC
09283fc updated axis limits 06 October 2020, 02:14:49 UTC
bba27de minor pipeline fix #2 05 October 2020, 23:46:36 UTC
dcc396b minor pipeline fix 05 October 2020, 23:45:32 UTC
5df68fa updated axis limits in some c-value histogram plots and updated gene_analysis_pipeline to run new subtract-simulated histogram code 05 October 2020, 23:40:33 UTC
4ca37f7 new scripts for IF image analysis and for new c value histogram analysis 05 October 2020, 20:56:24 UTC
0e3e68a detailed README with full instructions for re-creating each analysis forthcoming 26 May 2020, 17:07:12 UTC
b76f959 added modified chromVAR code 26 May 2020, 01:37:20 UTC
13ddbba removed software folder temporarily 26 May 2020, 01:36:27 UTC
f5c5449 added omni-atac protocol and modified chromvar software that is needed to make motif analysis plots 26 May 2020, 01:21:27 UTC
5f77c6c plumbing error fix 24 May 2020, 03:58:16 UTC
fe64efb new null distribution for estimating an expected dual motif match rate 24 May 2020, 03:56:40 UTC
9609756 added svg file suffix to plot outputs 13 May 2020, 00:20:33 UTC
9cf88a3 bug fix for pipeline argument name 13 May 2020, 00:19:01 UTC
c8e0adc added number of motifs per peak type script 13 May 2020, 00:17:40 UTC
c698205 added plumbing in pipeline for motif size and density plots (by motif combined response behavior category) 13 May 2020, 00:09:10 UTC
e9c4b34 added print statement to monitor progress 12 May 2020, 19:12:15 UTC
3b71749 changed y axis for one plot metric from frequency of peak types containing a motif to number of motifs per 150 bp of sequence of different peak types 12 May 2020, 18:16:59 UTC
9102618 added number of motif matches per peak to annotated output file 12 May 2020, 16:51:25 UTC
fc47f98 bug fix 07 May 2020, 22:26:33 UTC
9c62b97 changed layout of composed plots from horizontal to vertical 07 May 2020, 22:20:37 UTC
adfbfd5 typo fix in d val plot name 07 May 2020, 22:14:08 UTC
67137e1 updated file names and added composed plot of multiplicative prediction d val histograms for peaks 07 May 2020, 22:13:09 UTC
019f87c added multiplicative d value prediction histograms 07 May 2020, 18:54:22 UTC
4a08d1f added chromVAR variability plots to new supplemental figure 06 May 2020, 06:28:43 UTC
0696585 minor bug fix 06 May 2020, 03:43:37 UTC
79072cd added new supplemental motif analysis plot for canonical TFs activated by each signal 06 May 2020, 03:39:50 UTC
c5e25d1 standardized x axes on histograms 04 May 2020, 02:35:46 UTC
8fc8390 minor bug fix 04 May 2020, 02:33:09 UTC
64d47f9 made new histogram plots to show had c value changes with dosage increases 04 May 2020, 02:30:54 UTC
8f714dd added t-test script for peak types near gene types, and changed mutual exclusive peak pair plot to frequency of genes with at least one peak pair 28 April 2020, 21:57:33 UTC
30417c5 added new tick mark-less plots for gene integration summary and null distributions, to make it easier to make them match exactly in illustrator 17 April 2020, 14:37:07 UTC
936b7e2 reverted histogram bin width back to original smaller bins for in gene integration summary plots 16 April 2020, 15:30:31 UTC
e1e9132 changed logic of mutual-exclusive peak plot to only require the major-effector peak to go up in medium dose to be considered a mutually exclusive peak 07 April 2020, 19:27:05 UTC
e82a2e4 fixed minor bug in gene integration pie chart summary plot, which was discarding ~15 genes from an optional threshold that was not being used 31 March 2020, 19:13:22 UTC
6c86c8c updated histogram bins, updated plot outputs from null distribution scripts, to account for group meeting feedback 17 March 2020, 15:34:07 UTC
d2eac12 moved gene and peak analysis pipeline scripts to project root directory 27 February 2020, 23:05:27 UTC
6fe102c changed threshold for upper reporting to percent of genes above c = 4 27 February 2020, 23:00:27 UTC
9010cd7 switched from bias-corrected deviation scores to fractional change in reads compared to ethanol controls for motif analysis, and standardized y axes for motif enrichment analysis results 25 February 2020, 21:59:44 UTC
74a2f41 added bootstrap error bars to all motif analysis plots 25 February 2020, 02:07:53 UTC
d542088 added gene mutual exclusivity score to annotation script 22 February 2020, 22:27:28 UTC
2fab2cb bug fix 22 February 2020, 18:15:41 UTC
ea7a513 added composite plot & fixed plumbing error 22 February 2020, 18:10:05 UTC
ac8792a updated plumbing to make motif analysis plots 22 February 2020, 18:01:20 UTC
515cbca removed two legacy files that we put the important parts of in to the motif analysis scripts 21 February 2020, 18:03:23 UTC
62801f0 added script for motif analysis plots 21 February 2020, 18:02:07 UTC
f178a88 changed number of variable motifs to the top 50 and added CTCF 20 February 2020, 22:48:39 UTC
f09e283 consolidated all peaks near genes analysis to a single script, with bootstrap 95 percent confidence intervals 20 February 2020, 15:54:08 UTC
4d9c517 bug fix 20 February 2020, 00:49:49 UTC
d505269 adding mutual exclusive pairs of peak analysis 20 February 2020, 00:45:45 UTC
a02842f updated dimensions of patchwork plot 19 February 2020, 20:46:59 UTC
f66bed4 plumbing fix 19 February 2020, 20:36:38 UTC
c7d769e added bootstrap error bars to peaks near genes analysis plots, as well as a new patchwork-based layout for the 3x3 grid of peaks near genes plots 19 February 2020, 20:33:28 UTC
89955e9 added pie charts for med and high doses 18 February 2020, 22:24:12 UTC
1601031 syntax error fix 18 February 2020, 22:20:41 UTC
9d2c38a added code for making peak integration pie charts 18 February 2020, 22:19:22 UTC
e237a8d minor plumbing changes 18 February 2020, 21:35:43 UTC
90f6388 added ZNF469, an ambiguous gene, to the list of beeswarm plot genes 17 February 2020, 14:49:56 UTC
a1d3826 removed automatic y axis scaling from util.R 17 February 2020, 14:14:32 UTC
8fa0287 fixed automatic y axis label in null distribution script and added option to not standardize y axis in gene integration summary plots 17 February 2020, 14:11:35 UTC
ccee731 updated plumbing for making histograms for the observed data's c values 16 February 2020, 22:03:57 UTC
ad2d8ff null distributions for C values are now also plotted in a single final 3x3 grid 16 February 2020, 21:59:05 UTC
35e42c2 added support for plotting frequency instead of counts in figure 1 histograms 16 February 2020, 20:01:28 UTC
98b91aa increased granularity of null distributions, number of samples 15 February 2020, 21:30:36 UTC
0e81c6f bug fix 15 February 2020, 21:26:13 UTC
171b32c plumbing fix, gene analysis pipeline 15 February 2020, 21:19:57 UTC
b9fbc2e test 15 February 2020, 21:16:20 UTC
7031b64 plumbing fix 15 February 2020, 21:04:32 UTC
7a32ed2 updates to histogram plotting functions, created new util.R file to host shared functions between scripts, updates to null distribution calculations 15 February 2020, 21:00:53 UTC
f24e715 second attempt, remove filter for c value histograms 14 February 2020, 23:23:51 UTC
6758aeb removed filters for c value histograms and updated view of output c value histograms 14 February 2020, 23:20:25 UTC
75f2e52 plumbing fix 14 February 2020, 15:45:06 UTC
8e36d56 peak analysis pipeline fix. attempting to remove spurious log files from venn diagram script. 14 February 2020, 15:41:46 UTC
9f858ed added VennDiagram package back to venn diagram script as it's still being used... 14 February 2020, 15:37:23 UTC
54f5929 peak analysis pipeline bug fix 14 February 2020, 15:34:04 UTC
872a6f4 added making venn diagrams of differential genes and peaks to peak analysis pipeline 14 February 2020, 15:31:17 UTC
577c72a fixed order of categories in gene integration summary pie charts 13 February 2020, 00:45:08 UTC
833d632 added new script to measure the number of signal-exclusive peaks near genes of different integration categories 12 February 2020, 21:03:38 UTC
7a6dbec updated aesthetics of null distribution plots 11 February 2020, 23:40:45 UTC
e22a392 updated peak analysis pipeline to create null d value histograms 11 February 2020, 23:38:50 UTC
b9ed5a0 first commit for new null distributions script. updated gene analysis pipeline but not the peak analysis pipeline (yet) 11 February 2020, 23:13:45 UTC
4fa20d7 fixed error where i flipped the sign of a residual calculation 10 February 2020, 21:18:20 UTC
d7e9057 updated bug involving combining factors with strings 10 February 2020, 20:19:37 UTC
fdae22d added CTCF and SIX1 to motif set for exploratory analysis. CTCF was enriched in subadditive peaks and SIX1 was enriched in additive peaks in homer de novo motif analysis 10 February 2020, 20:02:25 UTC
7a1a1c4 added new scripts for looking at effect of motif on integration at a peak, as well as for making null distributions for c and d values. still under development. 09 February 2020, 22:11:58 UTC
85b093a peak analysis pipeline plumbing fix 08 February 2020, 23:37:12 UTC
bec941b peak analyis pipeline bug fix 08 February 2020, 23:24:28 UTC
24d4e53 removed minimum TPM from peaks near genes plot script and added option to run all steps of the pipeline without checking if files exist to peak analysis pipeline 08 February 2020, 01:06:06 UTC
3fad0e0 added shell script to run both gene and peak analysis pipelines 08 February 2020, 00:58:23 UTC
1d35bf7 added a new plot, number of all upregulated peaks near upregulated genes 08 February 2020, 00:50:47 UTC
6bad410 second attempt at last bug 08 February 2020, 00:49:17 UTC
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