From 7fedae5c21ff6e77841727663266b676d6578502 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Tue, 9 Dec 2025 14:58:43 -0500 Subject: [PATCH 1/5] Create README.md Generated initial draft of UCSC Genome Browser visualization information. --- genomeBrowserViz/README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 genomeBrowserViz/README.md diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md new file mode 100644 index 0000000..b7cd531 --- /dev/null +++ b/genomeBrowserViz/README.md @@ -0,0 +1,13 @@ +## UCSC Genome Browser Visualizations +Track data hubs can be used to visualize genomics signal tracks using the UCSC Genome Browser (for more information, please see the [Raney et al., 2014 (https://academic.oup.com/bioinformatics/article/30/7/1003/232409)] publication. + +We developed a track data hub to visualize maxATAC-derived _in-silico_ ChIP-seq datasets in tandem with chromatin accessibility data. Data can be explored in multiple ways using this tool. + +### Visualization of Genomic Regions +After loading the track data hub (link [here]) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website (https://genome.ucsc.edu/index.html)], you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of : + +### Identification of Specific TFBS +Right-clicking on the maxATAC prediction track (as demonstrated below) expands the composite track such that all TFs with binding sites in that region can be visualized. + +### Visualization of Specific Subpopulations +If you would like to visualize maxATAC predictions for a subset of subpopulations (e.g., the Th1 resting and active subpopulations), click on the... and select the desired subopoulations to visualize. From 4f9ac2662a9c9f173bdbc368f5bd60f5e8f04573 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Tue, 9 Dec 2025 14:59:04 -0500 Subject: [PATCH 2/5] Update README.md --- genomeBrowserViz/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index b7cd531..138bd94 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -1,5 +1,5 @@ ## UCSC Genome Browser Visualizations -Track data hubs can be used to visualize genomics signal tracks using the UCSC Genome Browser (for more information, please see the [Raney et al., 2014 (https://academic.oup.com/bioinformatics/article/30/7/1003/232409)] publication. +Track data hubs can be used to visualize genomics signal tracks using the UCSC Genome Browser (for more information, please see the [Raney et al., 2014](https://academic.oup.com/bioinformatics/article/30/7/1003/232409) publication. We developed a track data hub to visualize maxATAC-derived _in-silico_ ChIP-seq datasets in tandem with chromatin accessibility data. Data can be explored in multiple ways using this tool. From a63d0d10274d570c213d7b9f4050bf6c228c1303 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Tue, 9 Dec 2025 14:59:29 -0500 Subject: [PATCH 3/5] Update README.md --- genomeBrowserViz/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index 138bd94..d664038 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -4,7 +4,7 @@ Track data hubs can be used to visualize genomics signal tracks using the UCSC G We developed a track data hub to visualize maxATAC-derived _in-silico_ ChIP-seq datasets in tandem with chromatin accessibility data. Data can be explored in multiple ways using this tool. ### Visualization of Genomic Regions -After loading the track data hub (link [here]) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website (https://genome.ucsc.edu/index.html)], you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of : +After loading the track data hub (link [here]) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website](https://genome.ucsc.edu/index.html), you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of : ### Identification of Specific TFBS Right-clicking on the maxATAC prediction track (as demonstrated below) expands the composite track such that all TFs with binding sites in that region can be visualized. From 87031bfd549f4ffb47723024cdc123bc2f6d9800 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Tue, 16 Dec 2025 13:03:20 -0500 Subject: [PATCH 4/5] Update README.md --- genomeBrowserViz/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index d664038..dd59b54 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -4,7 +4,7 @@ Track data hubs can be used to visualize genomics signal tracks using the UCSC G We developed a track data hub to visualize maxATAC-derived _in-silico_ ChIP-seq datasets in tandem with chromatin accessibility data. Data can be explored in multiple ways using this tool. ### Visualization of Genomic Regions -After loading the track data hub (link [here]) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website](https://genome.ucsc.edu/index.html), you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of : +After loading the track data hub (link [here]) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website](https://genome.ucsc.edu/index.html), you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of _IFNG_: ### Identification of Specific TFBS Right-clicking on the maxATAC prediction track (as demonstrated below) expands the composite track such that all TFs with binding sites in that region can be visualized. From 2943c571163a126840bf8acd0dfabcd803fe3ba4 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Mon, 22 Dec 2025 21:07:12 -0500 Subject: [PATCH 5/5] Update README.md --- genomeBrowserViz/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index dd59b54..9815869 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -4,7 +4,7 @@ Track data hubs can be used to visualize genomics signal tracks using the UCSC G We developed a track data hub to visualize maxATAC-derived _in-silico_ ChIP-seq datasets in tandem with chromatin accessibility data. Data can be explored in multiple ways using this tool. ### Visualization of Genomic Regions -After loading the track data hub (link [here]) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website](https://genome.ucsc.edu/index.html), you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of _IFNG_: +After loading the track data hub (link [here](https://gb.research.cchmc.org/hub/group/memoryCD4/hub.txt)) in "My Data" > "Track Hubs" on the [UCSC Genome Browser website](https://genome.ucsc.edu/index.html), you can select specific genomic locations to visualize all subpopulation-resolved maxATAC predictions and chromatin accessibility information in that area. The image below shows the promoter and gene body of _IFNG_: ### Identification of Specific TFBS Right-clicking on the maxATAC prediction track (as demonstrated below) expands the composite track such that all TFs with binding sites in that region can be visualized.