AIBS version merge - bug fixes, clarification, feature adds, and refactor to object-oriented execution#8

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PRNicovich wants to merge 54 commits intoZhuangLab:masterfrom AllenInstitute:master

+274,077-89

Commits on Jun 17, 2019

Updated files to support mouse transcriptome building.
ScanningLabAnalysis
committed
Added required input files to build mouse probe set.
ScanningLabAnalysis
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Update README for forked repo.
ScanningLabAnalysis
committed
Added file to make FPKM_tracking file from input transcriptome.
ScanningLabAnalysis
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Update README.md
PRNicovich
authored

Commits on Jun 18, 2019

Added library_design_example.m file to repo.
ScanningLabAnalysis
committed
Merge branch 'master' of https://github.com/AllenInstitute/MERFISH_analysis
ScanningLabAnalysis
committed

Commits on Jun 20, 2019

Explicitly call out parameters for overlap, salt concentration, and probe concentration for TRDesigner input.wq
ScanningLabAnalysis
committed

Commits on Sep 20, 2019

Commit to AIBS stash repo w/ modifications.
Rusty Nicovich
committed

Commits on Sep 24, 2019

Including features for object-oriented execution of library design.
Rusty Nicovich
committed
Modified format in README.md.
Rusty Nicovich
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Continued fussing with README.md format.
Rusty Nicovich
committed
More work on README.md file.
Rusty Nicovich
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Modified .gitignore file.
Rusty Nicovich
committed
Added example readouts and fpkm_tracking files.
Rusty Nicovich
committed
Add example hypothalamus codebook file.
Rusty Nicovich
committed

Commits on Jan 3, 2020

Commits on Jan 6, 2020

Corrected issue leading to out of memory error with human transcriptome.
Rusty Nicovich
committed

Commits on Jan 8, 2020

Commits on Jan 14, 2020

Commits on Jan 22, 2020

Modified probeDesign.m to correctly include 'species' info.
Rusty Nicovich
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Commits on Jan 28, 2020

Added flags to MERFISHProbeDesign, probeDesign for specifyReadouts.
Rusty Nicovich
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Commits on Jan 30, 2020

Commits on Feb 7, 2020

Added file fileIO/permuteBySequence.m. Function allows generating
Rusty Nicovich
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Update MERFISHProbeDesign.m, probeDesign.m to reflect changes necessary
Rusty Nicovich
committed
Merge pull request #4 from AllenInstitute/readoutOrderSpecified
PRNicovich
authored

Commits on Feb 12, 2020

Commits on Feb 13, 2020

Commits on Feb 18, 2020

Commits on Apr 10, 2020

Commits on Apr 16, 2020

Added individual functions to filter TargetRegions object by common
Rusty Nicovich
committed

Commits on Apr 20, 2020

Updated probeDesign object, executeProbeDesign, MERFISHProbeDesign to
Rusty Nicovich
committed
Update README.md to include targetRegions filtering items.
Rusty Nicovich
committed
Additional updates of README.md to include targetRegions filtering parameters.
Rusty Nicovich
committed

Commits on Apr 27, 2020

Fixed error that crashed findFilteredTargetRegions.m when no target
Rusty Nicovich
committed

Commits on Apr 29, 2020

Modify MERFISHProbeDesign and probeDesign to support a [min, max] range
Rusty Nicovich
committed

Commits on May 5, 2020

Fixed issue in findCommonTargetRegions.m where min number of returned target regions would be minValue + 1, not minValue. Changed <= in if statements leading to break or continue to <.
Rusty Nicovich
committed

Commits on May 6, 2020

Merge pull request #9 from AllenInstitute/targetRegionsFilters
yilinzhao1615
authored

Commits on Jan 7, 2021

GH-192 Speed up saving target regions fasta file
sgratiy
committed