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--- 4dn:phase1:working_groups:data_analysis [2019/01/25 14:16]
rcalandrelli [Meetings]
+++ 4dn:phase1:working_groups:data_analysis [2025/04/22 16:21] (current)
@@ Line 1: / Line 1: @@
 ====== Data Analysis ======
+<font 20px/inherit;;#e74c3c;;inherit>**The mailing list for the working group has been changed. Please use [[analysis@4dnucleome.org]] from now on as the new mailing list address.**</font>
 ===== Introduction =====
@@ Line 23: / Line 25: @@
 ===== WebEx Meeting Information =====
-<font 20px/inherit;;inherit;;inherit>**Weekly Call - 4DN JAWG/DAWG Meeting\\
+<font 20px/inherit;;inherit;;inherit>**Weekly Call - 4DN JAWG/DAWG Meeting Every Thursday（from March 1, 2018)**</font>
-Every Thursday（from March 1, 2018)**</font>
 **1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time) **
-[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m8ea943b4f866758ce61e412a002a8a95&sa=D&sntz=1&usg=AFQjCNF6uGcS20RnYEw3eNQCt5LdpcpmcQ|Click here to Join WebEx meeting]]\\
+[[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m8ea943b4f866758ce61e412a002a8a95&sa=D&sntz=1&usg=AFQjCNF6uGcS20RnYEw3eNQCt5LdpcpmcQ|Click here to Join WebEx meeting]]\\ Meeting number: 805 283 801\\ Meeting password: uJe93m63\\ Host key: 347076
-Meeting number: 805 283 801\\
-Meeting password: uJe93m63\\
-Host key: 347076
-**Join by phone** \\
+**Join by phone**\\ +1-415-655-0002 US Toll
-+1-415-655-0002 US Toll
 Access code: 805 283 801
@@ Line 43: / Line 40: @@
 <font inherit/inherit;;#2980b9;;inherit>**858-822-1626 (OFFICE)**</font>
-<font inherit/inherit;;#2980b9;;inherit>**619-734-5961 (CELL)**</font>
 ===== Meetings =====
-\\
+\\ **1/13/2016**
-**1/13/2016**
+  * **Links: **
+      * [[https://docs.google.com/document/d/1rjYIXarELOkSWwDjsejTeWHotVKIlydGR2XIsI3Nyw4/edit?usp=sharing|google doc page]].
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6N2UxYWQ3Nzk0N2U2MTg4NQ|Additional notes]].
-**Links: **
+\\ **3/4/2016 **
+  * **Agenda:**
+      * Dekker lab HiC pipeline - Bryan Lajoie
+  * **Links:**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MmU1ZjMxM2ZlOGFiMGU5NQ|presentation]].
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NjNjNTAzYzAzZjI1MGZhZA|Some notes]]
-   * [[https://docs.google.com/document/d/1rjYIXarELOkSWwDjsejTeWHotVKIlydGR2XIsI3Nyw4/edit?usp=sharing|google doc page]].
+**4/26/2016**
-  * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6N2UxYWQ3Nzk0N2U2MTg4NQ|Additional notes]].
+  * **Agenda:**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NzE3MzIxNWQ2NWZmYTQ3MA|Presentation on Hi-C quality and reproducibility metrics]] by Gurkan Yardimci from Bill Noble's group.
+  * **Links:**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NzE3MzIxNWQ2NWZmYTQ3MA|Slides]].
+      * [[https://docs.google.com/document/d/1Wojo6GG0VxXx17heUH9r1idltQlQV_718A0Aq-XvtN4/edit?usp=sharing|Additional notes.]]
- \\ **3/4/2016 **
+**7/20/2016**
 **Agenda:**
+  * AWG+OMICS call. Presentations on loop detection from Erez Lieberman and [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/data-analysis-wg/Gold Standard Discussion Ren 072016.pptx?attredirects=0|Bing Ren]]'s groups.
-  * Dekker lab HiC pipeline - Bryan Lajoie
 **Links:**
+  * [[http://www.google.com/url?q=http://pklab.med.harvard.edu/peterk/4dn/awg/AWG+OMICS joint call  benchmarking  loop detection-20160720 1629-1.arf&sa=D&sntz=1&usg=AFQjCNGi9pT8824uLCPV3VP_zGzftxV20w|Webex recording]].
+  * [[https://docs.google.com/document/d/193FF2DJklhoBf7-bf0UgYeBeKkB2ThfffGxi9JY2WGw/edit|Minutes]].
-  * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MmU1ZjMxM2ZlOGFiMGU5NQ|presentation]].
+**8/3/2016**
-  * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NjNjNTAzYzAzZjI1MGZhZA|Some notes]]
+  * **Agenda:**
+      * AWG+OMICS call. Presentation from Yijun Ruan's group
+  * **Links:**
+      * [[http://www.google.com/url?q=http://pklab.med.harvard.edu/peterk/4dn/awg/OMICS+AWG call 2  loop-based benchmarking-20160803 1600-1.arf&sa=D&sntz=1&usg=AFQjCNH5128cbaaySVTTM7AUfbQP8qn24A|Webex recording]].
-**4/26/2016**
+**9/29/2016 **
+  * **Links:**
+      * [[https://docs.google.com/document/d/18meAIDn-m5j5dITktPiq7IW1tT9VoLigZkqILJoeSCE/edit?usp=sharing|Minutes]].
-**Agenda:**
+**1/26/2017 **
+  * **Agenda:**
+      * HiC reproducibility metrics - Gurkan Yardimici from Bill Noble's group.
+  * **Links:**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo3MTczMjE1ZDY1ZmZhNDcw|Slides]].
-  * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NzE3MzIxNWQ2NWZmYTQ3MA|Presentation on Hi-C quality and reproducibility metrics]] by Gurkan Yardimci from Bill Noble's group.
+**3/23/2017**
+  * **Agenda:**
+      * Presentation by DCIC on uniform pipeline status and plans.
+  * **Links:**
+      * [[https://drive.google.com/file/d/0B6cuZNSltxB9Z2FFdHBvR2FhYkE/view|Slides]].
+      * [[https://docs.google.com/document/d/1FTa1Z-LhTvQ96EtNkl4ziOX-xE6WvMuco_97Eg6Pwas/edit#|Google Doc]].
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=4ec05ba389507b37a3391145fb00f64d&sa=D&sntz=1&usg=AFQjCNH30uLLcUMxUN7SFdphnfonvZsnFQ|Webex recording]].
-**Links:**
+**4/6/2017 **
+  * **Agenda:**
+      * Presentation by Michael Sauria (James Taylor lab) on Hi-C reproducibility analysis
+  * **Links:**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyNDc1YzM2ZmY4ODRhOTdl|Slides]].
+      * [[https://docs.google.com/document/d/1ASbJWYKiQVkGczmSdx4m760UL-r4hoF8v6Fcj_rmYx8/edit?usp=sharing|Google Doc]].
-  * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6NzE3MzIxNWQ2NWZmYTQ3MA|Slides]].
+**4/20/2017**
-  * [[https://docs.google.com/document/d/1Wojo6GG0VxXx17heUH9r1idltQlQV_718A0Aq-XvtN4/edit?usp=sharing|Additional notes.]]
+  * **Agenda:**
+      * DCIC updates / alignment (10minutes)
+      * Presentation by Ren lab on Normalization (20min)
+      * Discussion (10 minutes)
+  * **Links:**
+      * [[https://docs.google.com/document/d/16JFF_1IoEfmp8ns8kVhxK9n1eexENhv26lSgTA_96Ws/edit?usp=sharing|Minutes.]]
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=f00ca90cefe175a0493d6708b78cb2b8&sa=D&sntz=1&usg=AFQjCNGXxgex_vvdyOZVwEGipjcEoG-96A|Webex recording.]]
-**7/20/2016**
+**5/4/2017**
+  * **Agenda:**
+      * DCIC updates (5minutes)
+      * Presentation by Aiden lab on Normalization (20min)
+      * Presentation by Mirny lab on Normalization (20min)
+      * Discussion: what is needed for consensus? (15min)
+  * **Links:**
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=f00ca90cefe175a0493d6708b78cb2b8&sa=D&sntz=1&usg=AFQjCNGXxgex_vvdyOZVwEGipjcEoG-96A|Recording.]]
-**Agenda:**
+**5/18/2017**
+  * **Agenda:**
+      * Presentation by Francesco Ferrari on TAD callers
+  * **Links:**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo0OGIxZDFiOTQ4NmY1MmI4|Slides]].
+      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170518|DAWG Meeting Notes 20170518]].
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=179d1cdde5f4241f3b962f58f7b2c971&sa=D&sntz=1&usg=AFQjCNE942yNVAl2Sgg0mPlktnz5m3-d3w|Recording]].
+      * [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/data-analysis-wg/Ferrari_TADcalls.rar?attredirects=0&d=1|TAD calls.]]
-  * AWG+OMICS call. Presentations on loop detection from Erez Lieberman and [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/working-groups-list/data-analysis-wg/Gold Standard Discussion Ren 072016.pptx?attredirects=0|Bing Ren]]'s groups.
+**6/1/2017**
+  * **Agenda:**
+      * Read filtering I: Mirny lab.
+  * **Links:**
+      * [[https://docs.google.com/presentation/d/1oZDoFMEFKz8JQUy-hx4roWcU_zP_9lzp2FwRuROkWEc/edit#slide=id.p|Slides]].
+      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170601|DAWG Meeting Notes 20170601]].
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=fc5b4225a0e391dd0ba2af58c1ff9a16&sa=D&sntz=1&usg=AFQjCNHTzMaG1VOA-T139mcvo2l8KAo1YA|Recording]].
-**Links:**
+**6/15/2017**
+  * **Agenda**
+      * DCIC updates
+      * Read filtering II
+  * **Links**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyYzJmNzYyZjJlMWZkZTg1|Slides]].
+      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170615|DAWG Meeting Notes 20170615]].
-  * [[http://www.google.com/url?q=http://pklab.med.harvard.edu/peterk/4dn/awg/AWG+OMICS joint call  benchmarking  loop detection-20160720 1629-1.arf&sa=D&sntz=1&usg=AFQjCNGi9pT8824uLCPV3VP_zGzftxV20w|Webex recording]].
+**7/13/2017**
-  * [[https://docs.google.com/document/d/193FF2DJklhoBf7-bf0UgYeBeKkB2ThfffGxi9JY2WGw/edit|Minutes]].
+  * **Agenda**
+      * Continuing on: Presentation by Francesco Ferrari on TAD callers
+      * Please write to Peter_Kharchenko@hms.harvard.edu if you would like to present
+  * **Links**
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=c4a1d3568d4d50315b85220c44f3a9bb&sa=D&sntz=1&usg=AFQjCNH0DGRrtHz7xvOvac43z3FgaC5XlQ|Recording.]]
-**8/3/2016**
+**8/3/2017**
+  * **Agenda**
+      * TAD Callers: continued discussion
+      * Visualization of TADs
+        * Peter Kerpedjiev (Gehlenborg lab) - HiGlass
+        * Neva C Durand (Aiden Lab) - Arrowhead/Juicebox
+  * **Links**
+      * [[https://docs.google.com/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2ZDgyYzEwYTdiNjEwNGUx|Arrowhead Slides]].
+      * [[4dn:phase1:data_analysis:dawg-meeting-notes-20170803|DAWG Meeting Notes 20170803]].
+      * [[https://www.google.com/url?q=https://4dnucleome.webex.com/4dnucleome/ldr.php?RCID=920d2ead6e130d3560c557271acea7cc&sa=D&sntz=1&usg=AFQjCNGyIM_k4bR0ZbsOqKYA0Sw7ORcMZQ|Recording]].
-**Agenda:**
+**9/7/2017 **
+  * **Agenda**
+      * Defining contact domains: CTCF and cohesion depletion
+        * Mirny Lab
+        * Aiden Lab
-  * AWG+OMICS call. Presentation from Yijun Ruan's group
+===== Members (original list) =====
-**Links:**
+<font 20px/inherit;;inherit;;inherit>Co-Chairs:</font>
-  * [[http://www.google.com/url?q=http://pklab.med.harvard.edu/peterk/4dn/awg/OMICS+AWG call 2  loop-based benchmarking-20160803 1600-1.arf&sa=D&sntz=1&usg=AFQjCNH5128cbaaySVTTM7AUfbQP8qn24A|Webex recording]].
+<font 20px/inherit;;inherit;;inherit>Peter Kharchenko, <peter_kharchenko@hms.harvard.edu>
+William Noble, <wnoble@uw.edu></font>
-**9/29/2016 **
+<font inherit/inherit;;inherit;;#e74c3c>Insert data analysis members spreadsheet</font>
-**Links:**
+**Program Staff**
+Weizhong Chen, PhD <wec125@eng.ucsd.edu>
+This can be a list of all other working members in the working group.
+===== Mailing list =====
+The mailing list to use for communication in this Working Group is <analysis@4dnucleome.org>. Emails sent there will go to everyone on the list. Replying to an email from the list will also send it to everyone in the list.
-  * [[https://docs.google.com/document/d/18meAIDn-m5j5dITktPiq7IW1tT9VoLigZkqILJoeSCE/edit?usp=sharing|Minutes]].
+===== Calendar =====
-/26/2017 HiC reproducibility metrics - Gurkan Yardimici from Bill Noble's group. Slides. \\ 3/23/2017 Presentation by DCIC on uniform pipeline status and plans. Slides. Google Doc. Webex recording. \\ 4/6/2017 Presentation by Michael Sauria (James Taylor lab) on Hi-C reproducibility analysis Slides. Google Doc. \\ 4/20/2017 \\ DCIC updates / alignment (10minutes) \\ Presentation by Ren lab on Normalization (20min) \\ Discussion (10 minutes) \\ Minutes. Webex recording. \\ 5/4/2017 \\ DCIC updates (5minutes) \\ Presentation by Aiden lab on Normalization (20min) \\ Presentation by Mirny lab on Normalization (20min) \\ Discussion: what is needed for consensus? (15min) \\ Recording. \\ 5/18/2017 \\ Presentation by Francesco Ferrari on TAD callers \\ Slides. DAWG Meeting Notes 20170518. Recording. \\ TAD calls. \\ 6/1/2017 \\ Read filtering I: Mirny lab. \\ Slides. DAWG Meeting Notes 20170601. Recording. \\ 6/15/2017 \\ DCIC updates \\ Read filtering II \\ Slides. DAWG Meeting Notes 20170615. \\ 7/13/2017 \\ Continuing on: Presentation by Francesco Ferrari on TAD callers \\ Please write to Peter_Kharchenko@hms.harvard.edu if you would like to present \\ Recording. \\ 8/3/2017 \\ TAD Callers: continued discussion \\ Visualization of TADs \\ Peter Kerpedjiev (Gehlenborg lab) - HiGlass \\ Neva C Durand (Aiden Lab) - Arrowhead/Juicebox \\ Arrowhead Slides. DAWG Meeting Notes 20170803. Recording. \\ 9/7/2017 Defining contact domains: CTCF and cohesion depletion \\ - Mirny Lab \\ - Aiden Lab
+{{url>https://calendar.google.com/calendar/embed?src=l83jh4t35tpd46ad6dq822ck78%40group.calendar.google.com&ctz=America%2FLos_Angeles 800,400 noborder|4DN Data Analysis WG Calendar}}

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