greenelab/core-accessory-interactome issues and pull requests

#63 - Combine Figures S2 and S3

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#62 - Manuscript revisions

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#61 - Update figure 1

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#60 - Add revisions based on reviewer comments

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#59 - Additional exploration

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 2 comments

#58 - Update figures for manuscript

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago - 2 comments

#57 - Figure and readme updates

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago

#56 - Update analysis based on co-authors comments

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago - 2 comments

#55 - Update readme

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago

#54 - Another analysis reun and update figure 1

Pull Request - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#53 - Redo analysis using latest version of compendia

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#52 - Update manuscript figures and fix distance calculation

Pull Request - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#51 - Make draft manuscript figures

Pull Request - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#50 - Update core-core and core-acc analyses

Pull Request - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#49 - Refactor and redo analyses using SPELL correlation matrix

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#48 - Compare SPELL vs counts correlation

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#47 - Extend stability

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#46 - Add scripts and analysis nbs from SOPHIE

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#45 - Minor refactor

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#44 - Add more exploratory analysis from discussion with collaborator

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#43 - Refactor

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#42 - Add analyses examining accessory genes

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#41 - Create figures and data for Georgia's manuscript

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#40 - Add enrichment analysis of modules

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#39 - Minor refactor and quantify common DEG analysis

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#38 - Lookup samples for Georgia's manuscript

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#37 - Validate that correlation modules are biologically relevant

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#36 - Get acc-acc modules and annotate

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#36 - Get acc-acc modules and annotate

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#35 - Add analysis to compare core-core modules across strains

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#34 - Refactor to prepare for separate module analysis

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#33 - Compare relationships using genome distance vs expression distance

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#32 - Re-run analysis using new QCd data

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#31 - common DEGs and core/acc annotations

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#30 - Calculate module composition

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#29 - Add community detection and random walk approaches

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#28 - Update validation scripts

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#27 - Update clustering scripts

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 4 comments

#26 - Update threshold for compendia and reprocess

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#25 - Apply correlation correction

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago

#24 - Simplify network analysis

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago

#23 - Network validation

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago - 1 comment

#22 - Considerations for tuning network

Issue - State: open - Opened by ajlee21 almost 4 years ago

#21 - Add network analysis

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago - 1 comment

#20 - Bin samples using accessory gene expression

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago - 1 comment

#19 - Create expression compendia based on mapping rates

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago - 1 comment

#18 - Explore data

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago - 1 comment

#17 - Quick reorganization

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago

#16 - Add clustering analysis of accessory genes for PAO1 and PA14 compendia

Pull Request - State: closed - Opened by ajlee21 almost 4 years ago - 2 comments

#15 - Add exploratory analysis

Pull Request - State: closed - Opened by ajlee21 about 4 years ago - 1 comment

#14 - Create phage+PAO1 reference genome

Pull Request - State: closed - Opened by ajlee21 about 4 years ago - 1 comment

#13 - Add details about how Salmon works

Pull Request - State: closed - Opened by ajlee21 about 4 years ago - 1 comment

#12 - Continue testing phage reference genome

Pull Request - State: closed - Opened by ajlee21 about 4 years ago - 3 comments

#11 - Test phage reference genome

Pull Request - State: closed - Opened by ajlee21 about 4 years ago - 1 comment

#10 - Add DE validation analysis

Pull Request - State: closed - Opened by ajlee21 over 4 years ago

#9 - Rnaseq corr

Pull Request - State: closed - Opened by ajlee21 over 4 years ago

#8 - Add salmon processing pipeline

Pull Request - State: closed - Opened by ajlee21 over 4 years ago - 3 comments

#7 - Compare correlated genes

Pull Request - State: closed - Opened by ajlee21 over 4 years ago

#6 - Quantify difference in likelihood

Issue - State: open - Opened by ajlee21 over 4 years ago

#5 - Correlation of genes in different partitions

Pull Request - State: closed - Opened by ajlee21 over 4 years ago

#4 - Coexpression analysis

Pull Request - State: closed - Opened by ajlee21 almost 5 years ago

#3 - Is accessory shift consistent across other groups of samples?

Issue - State: open - Opened by ajlee21 almost 5 years ago

#2 - Try calculating correlations using only PAO1 samples and only PA14 samples

Issue - State: closed - Opened by ajlee21 almost 5 years ago - 1 comment

#1 - First pass analysis of core-accessory relationships

Pull Request - State: closed - Opened by ajlee21 almost 5 years ago - 2 comments

GitHub / greenelab/core-accessory-interactome issues and pull requests