AIBS version merge - bug fixes, clarification, feature adds, and refactor to object-oriented execution #8
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Multitude of error corrections throughout original code. Added ./outputForLIMS/ folder for helper scripts to convert MATLAB output to LIMS output. However - Python library 'mFISHCodebookPermutation/ is current supported version of these functins.
…alysis Merge in remote repo README edits.
…robe concentration for TRDesigner input.wq
./MERFISH_Examples2/library_design_example.m now supplanted by ./probe_construction/MERFISHProbeDesign.m. Copy required files from matlab-storm.m to remove dependency on that library. Copied files in ./fileIO/. Edit README.md to include newly-named variables and default values.
this version works with LIMS references changed "transferAbund" to "true" under "if useUniformWeights" output the same probes each run
Transcriptome object now deleted after generating slicedTranscriptome, immediately before building TRDesigner object.
The human_MTG sequential codebook revealed a bug that the allOligos were not collected correctly with the original version. I rewrote the logic to collect allOligos.
1. Check whether gene and ids match with each other in the reference, send a warning if not 2. allOligos file is written in a different way to avoid empty cells when there are mismatched gene+ids in the codebook 3. change the selection process of probes to stop picking duplicated probes for genes with multiple transcripts
executeProbeDesign.m accumulating edits from use.
If true, will use ordering from codebook. If false, use ordering from readouts.fasta file. Will import settings from log file.
Pre-allocating TargetRegions object avoids duplication of array in 'flattening' step, bypasses memory error line. Fixed issues with 'debugMode' in MERFISHProbeDesign, TRDesigner. DebugMode on TRDEsigner.DesignTargetRegions actually does something now.
Modified TRDesigner.DesignTargetRegions to avoid out of memory errors.
pseudo-random order of readouts given a sequence of integer representations of characters.
for permuteBySequence to operate.
Readout order specified
Readout specified, memErrors fix
Mem errors
Tested. We can keep the ensemble and NCBI choice as long as we remove the NCBI _ to , modification.
Update MERFISHProbeDesign.m
Fixed the bug for smELT mode and added a table to list probe numbers generated for each gene.
readoutOrderSmELT
generated target regions.
regions, expanding acceptable isospecificity, or by a specified parameter range. Added targetRegionsFilteringDemo.m to demonstrate three methods to do TargetRegions filtering. Modified MERFISHProbeDesign, probeDesign, executeProbeDesign to support the new parameters.
support targetRegions filtering, spaceOutProbes parameters.
regions are returned. Cumulative sum of isospecificty values in findExpandedIsospecificityTargetRegions was backwards. Now corrected.
for numProbesPerGene.
… target regions would be minValue + 1, not minValue. Changed <= in if statements leading to break or continue to <.
Target regions filters
Buffer output data into a struct and save in chunks for every 100 genes Add progress information
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Have implemented a number of changes to support our work with MERFISH and probe design. Changes summarized below.
Have tested these changes on various panel builds and against demo code + input examples. I have confirmed that the probes generated with this edited fork are same as those in base repo w/ provided input files.
Key edits and notes: