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 01/10] 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 02/10] 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 03/10] 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 04/10] 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 05/10] 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. From 7e811c243dadaf944251188e25ee7a366ab24c7f Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Sun, 1 Feb 2026 23:22:32 -0500 Subject: [PATCH 06/10] Update README.md Added screenshots from UCSC Genome Browser. --- genomeBrowserViz/README.md | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index 9815869..028f6d7 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -1,13 +1,28 @@ ## 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. +We developed a track data hub to visualize both maxATAC-derived _in-silico_ and experimental 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](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_: +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. For instance, the image below shows maxATAC predictions in each of the sixteen subpopulations at 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. +![260201_CD4_T_Cell_UCSC_Genome_Browser_Screenshot](https://github.com/user-attachments/assets/c013db27-6829-47fa-962a-161b819814cf) ### 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. +If you would like to visualize maxATAC predictions for a subset of subpopulations (e.g., the Th1 resting and active subpopulations), navigate to the track settings page for this track and select the desired subopoulations to visualize, as shown below. + +260201_CD4_T_Cell_UCSC_Genome_Browser_Settings + +Once the changes are submitted, only the desired subpopulations appear in the Browser. + +![260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Screenshot](https://github.com/user-attachments/assets/d3c7938b-ca4f-48f8-9672-94f83c03d90f) + +### Identification of Specific TFBS +By right-clicking on one of the subpopulation tracks and selecting the "pack" option, you can visualize all TFs with predicted binding sites in that region for the chosen subpopulation. + +260201_CD4_T_Cell_UCSC_Genome_Browser_Settings_Two + +For example, the following screenshot demonstrates all of the TFs that are predicted to bind at one of the promoters of _IFNG_ in the resting Th1 subpopulation. + +![260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Rest_Screenshot](https://github.com/user-attachments/assets/386d0a5b-173b-4f49-9921-06ac818ab3be) + From f6f68cf712fa5595c1fa458601eef7a4eb312610 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Sun, 1 Feb 2026 23:27:17 -0500 Subject: [PATCH 07/10] Update README.md Fixed screenshot links. --- genomeBrowserViz/README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index 028f6d7..4dee842 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -6,7 +6,7 @@ We developed a track data hub to visualize both maxATAC-derived _in-silico_ and ### Visualization of Genomic Regions 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. For instance, the image below shows maxATAC predictions in each of the sixteen subpopulations at the promoter and gene body of _IFNG_. -![260201_CD4_T_Cell_UCSC_Genome_Browser_Screenshot](https://github.com/user-attachments/assets/c013db27-6829-47fa-962a-161b819814cf) +260201_CD4_T_Cell_UCSC_Genome_Browser_Screenshot ### 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), navigate to the track settings page for this track and select the desired subopoulations to visualize, as shown below. @@ -15,7 +15,7 @@ If you would like to visualize maxATAC predictions for a subset of subpopulation Once the changes are submitted, only the desired subpopulations appear in the Browser. -![260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Screenshot](https://github.com/user-attachments/assets/d3c7938b-ca4f-48f8-9672-94f83c03d90f) +260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Screenshot ### Identification of Specific TFBS By right-clicking on one of the subpopulation tracks and selecting the "pack" option, you can visualize all TFs with predicted binding sites in that region for the chosen subpopulation. @@ -26,3 +26,4 @@ For example, the following screenshot demonstrates all of the TFs that are predi ![260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Rest_Screenshot](https://github.com/user-attachments/assets/386d0a5b-173b-4f49-9921-06ac818ab3be) + From 3757549f4b57178f3315a52f4737cc61094ba440 Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Sun, 1 Feb 2026 23:31:18 -0500 Subject: [PATCH 08/10] Update README.md Fixed image. --- genomeBrowserViz/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index 4dee842..834a612 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -6,7 +6,7 @@ We developed a track data hub to visualize both maxATAC-derived _in-silico_ and ### Visualization of Genomic Regions 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. For instance, the image below shows maxATAC predictions in each of the sixteen subpopulations at the promoter and gene body of _IFNG_. -260201_CD4_T_Cell_UCSC_Genome_Browser_Screenshot +260201_CD4_T_Cell_UCSC_Genome_Browser_Screenshot ### 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), navigate to the track settings page for this track and select the desired subopoulations to visualize, as shown below. @@ -24,6 +24,6 @@ By right-clicking on one of the subpopulation tracks and selecting the "pack" op For example, the following screenshot demonstrates all of the TFs that are predicted to bind at one of the promoters of _IFNG_ in the resting Th1 subpopulation. -![260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Rest_Screenshot](https://github.com/user-attachments/assets/386d0a5b-173b-4f49-9921-06ac818ab3be) + From 37197852442ddd261f7093e5417e2a4534bf202a Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Mon, 2 Feb 2026 14:38:41 -0500 Subject: [PATCH 09/10] Update README.md Added final screenshot. --- genomeBrowserViz/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index 834a612..d5ae8a9 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -24,6 +24,7 @@ By right-clicking on one of the subpopulation tracks and selecting the "pack" op For example, the following screenshot demonstrates all of the TFs that are predicted to bind at one of the promoters of _IFNG_ in the resting Th1 subpopulation. +260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Rest_Screenshot From 19afbbe73a6266a0c960e54afe2f0b59284c378b Mon Sep 17 00:00:00 2001 From: "Akshata N. Rudrapatna" <139808049+ANRudrapatna@users.noreply.github.com> Date: Mon, 2 Feb 2026 14:39:50 -0500 Subject: [PATCH 10/10] Update README.md Edited text to be in correspondence with an image. --- genomeBrowserViz/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genomeBrowserViz/README.md b/genomeBrowserViz/README.md index d5ae8a9..d7b13cb 100644 --- a/genomeBrowserViz/README.md +++ b/genomeBrowserViz/README.md @@ -22,7 +22,7 @@ By right-clicking on one of the subpopulation tracks and selecting the "pack" op 260201_CD4_T_Cell_UCSC_Genome_Browser_Settings_Two -For example, the following screenshot demonstrates all of the TFs that are predicted to bind at one of the promoters of _IFNG_ in the resting Th1 subpopulation. +For example, the following screenshot demonstrates TFBS for all of the TFs that are predicted to bind at an _IFNG_ promoter in the resting Th1 subpopulation. 260201_CD4_T_Cell_UCSC_Genome_Browser_Th1_Rest_Screenshot