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Multiplex_Major_Patch#452

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andredsim wants to merge 217 commits intodevelGoekeLab/bambu:develfrom Multiplex_Major_PatchGoekeLab/bambu:Multiplex_Major_PatchCopy head branch name to clipboard

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Commits

Commits on Dec 1, 2022

• Remove SE from being combined during extendAnno

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Commits on Apr 17, 2023

• Copy over rowdata from equal read classes above NDR threshold

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• Add lowConfidenceTranscripts to metadata and speed up relSubsetCount

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• subset transcripts are added to metadata

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• Add helper function to set NDR on extendedAnnotations

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• function to set NDR threshold on extendedAnno

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• Revert "Add helper function to set NDR on extendedAnnotations"

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• export setNDR

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Commits on Apr 20, 2023

• readClass warnings kept only when rcFile is made and not when loaded in

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• set seqlevels of reads to only seqnames in the reads to reduce warnings

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Commits on Apr 26, 2023

• write NDR to gtf

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• Read in NDR if in gtf

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• Allow setNDR to work on gtf files that are read in

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• Allow NDR filtering in NDR quant only mode

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Commits on Apr 27, 2023

• Add txScore to mcols

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• read and write the txScore to GTF

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• NA's are loaded in as NAs from GTF

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• setNDR can now recommend NDR

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• Add documentation to setNDR and carry arguments over

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• Update test cases to include metadata and new warnings

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Commits on Apr 28, 2023

• Assign names to transcripts earler so subset and lowConf are given names

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• Remove unneeded argument

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  afc9e03

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• Fix includeRef bug

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• Unit tests for setNDR

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• Unit tests for reading and writing NDR and txScore

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Commits on May 3, 2023

• Update documentation

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  5be3a63

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• fix setNDR test

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Commits on May 9, 2023

• Bambu now outputs 3 gtf files by default

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• 4th GTF of novel transcripts only

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• Include options to ignore GTF outputs

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• Update documentation with writeAnnotationsToGTF

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Commits on Jun 13, 2023

• Fix typo

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Commits on Jun 26, 2023

• Fix typo

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  3466f7f

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• Fix typo

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  754e5ed

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• Fix bug when rcOutDir not used

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• Improve default outs to include counts of rcs and txs

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Commits on Jul 10, 2023

• Ensure eqClasses is recalculated when setting NDR

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Commits on Sep 26, 2023

• Use one read class file for multiple samples

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• quick fix hack to enable readGrgList as input

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Commits on Sep 28, 2023

• small temp hack to allow readClassInput for now

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• Move getUniCountPerEquiRC outside bplapply

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  5fae869

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• Speed up bambu.quant

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  22a8aaf

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• Clean up bambu.quantify and add calculateEqClassCounts

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  e7d3c7b

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• Tidy up code

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  136f9a6

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• Also tidy up

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Commits on Oct 2, 2023

• Fix issue where old memory was used

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• MessyForest

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• Merge branch 'combined_rcFile_rgrListHack' into messyForest

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Commits on Oct 3, 2023

• bug fix the merge

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  2456617

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• Clean up combining SEs

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Commits on Oct 4, 2023

• Enable demultiplexing and speed up splitReadClassFiles()

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  0623322

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• fix formatting issues

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  32b5692

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• fix bugs

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  c2b3bf5

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• Enable threading for demultiplexed samples

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• Remove progress bar

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• adapt threading for demultiplexing

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Commits on Oct 5, 2023

• Reduce memory input to threads

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• Reduce memory before threading

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Commits on Oct 6, 2023

• Clean up distTable code

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  8495cc8

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• Fix crash at end caused by sample names

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Commits on Oct 12, 2023

• add in missing variable

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Commits on Oct 19, 2023

• Instead calculate eqClass counts before parralellization

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Commits on Oct 20, 2023

• Speed up addAval

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  964fea8

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• Make readClassDt a data.table from the start

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  82dc9d4

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Commits on Oct 27, 2023

• Fix bug where counts were not assigned to correct transcripts

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• Missed line

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  9e5930f

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• Tidy up

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  1b664b1

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• Fix bug where reads were missing after splitReadClassFile

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  0e24641

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Commits on Oct 31, 2023

• Add in helper splitReadClassByRC for old functionality

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  1f22942

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Commits on Nov 1, 2023

• Fix bug caused by different sorting of unspliced reads

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  e890af9

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Commits on Nov 14, 2023

• Stop incompatibleCounts from being converted away from sparseMatrix

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  1ae237c

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• make transcriptToGene compatible with sparseMatrix

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Commits on Nov 15, 2023

• Enable Bambu to restart with readClassDt to help with R hogging memory

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  9ab0767

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• fix missing reference due to change

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  ff69eac

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Commits on Dec 1, 2023

• Resolve lack of incompatible rcs better

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Commits on Dec 4, 2023

• Insert missing fix for assignGeneIds

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  a1de0dc

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Commits on Dec 12, 2023

• reallow deg bias

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Commits on Dec 20, 2023

• Reenable writeBambuOutput

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  a8063cb

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Commits on Jan 5, 2024

• different bam input for CB

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Commits on Jan 16, 2024

• update quantification output file format

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  3d2b794

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Commits on Jan 19, 2024

• added spatial location information

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Commits on Jan 23, 2024

• updated gzfile function

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  77dae23

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• revert changes in gzfile

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  c78c793

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• added ifelse test for spatial

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Commits on Feb 2, 2024

• Enable fusion mode again

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• Remove warning about bambu annotations if discovery not being done

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Commits on Feb 8, 2024

• Keep readnames even if demultiplexed

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  c392d08

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• Enable messyForest to take in multiple samples

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Commits on Feb 21, 2024

• Add cleanRead argument

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Commits on Feb 29, 2024

• Tidy up clean reads

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Commits on Mar 5, 2024

• UMI deduplication

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Commits on Mar 12, 2024

• Merge branch 'devel' into remov_SE_combineAnno

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  04b5857

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• change order of UMI dedup with cleaning reads

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  26afc66

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• add extra messages

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Commits on Mar 19, 2024

• add in argument

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Commits on Apr 1, 2024

• Transcript discovery at cluster level

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Commits on Apr 5, 2024

• Merge branch 'devel' into remov_SE_combineAnno

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Commits on Apr 11, 2024

• keep txScore in extendAnno

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Commits on Apr 12, 2024

• Allow demultiplexing from file

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Commits on Apr 19, 2024

• Flexible BC and UMI lengths

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• Refactor CB to BC

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  28f2ca8

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Commits on Apr 25, 2024

• Seperate umi dedup from cleanReads

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Commits on Apr 29, 2024

• write rowData to gtf

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• read in attributes as rowData

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  ddc0ed9

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• Ensure assays stays a sparse matrix even if empty

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  31ca44d

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• Fix flexible barcode lengths

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  0336e6b

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• fix importing bam

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  6790ce7

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• importBambuOutput function

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  8bbb0a1

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Commits on Apr 30, 2024

• writeBambuOutput rights incompatibleCounts and can seperate samples

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Commits on May 2, 2024

• clean up warnings

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  c568679

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Commits on Jun 26, 2024

• Report all possible transripts if NDR = 1

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  0b47cb8

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Commits on Jul 22, 2024

• fix bug when reading in barcode map from file

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  fbe8ee3

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Commits on Aug 1, 2024

• catch error when no drate is calculated due to low reads

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Commits on Aug 13, 2024

• return non em counts before quant step

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Commits on Aug 21, 2024

• Fix the normal discovery impact cluster discovery

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Commits on Aug 23, 2024

• Enable clusters to be assigned before EM

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Commits on Aug 27, 2024

• Fix bug in denono

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• AssignDist step will now output uniqueCounts

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• Remove old gene count code

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Commits on Sep 2, 2024

• Update low memory to process read classes together or seperately

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• Can now provide multiple clusterings per quant input

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  716370c

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• tidy up

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  8fb23e0

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• clean up warnings

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Commits on Sep 3, 2024

• Make sure column names are present when providing clusters

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Commits on Sep 4, 2024

• fix colData bug missing names

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  87dc794

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• Track sample names into quantData

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  8931903

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• Fix clustering to work with different input combinations

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• bug fix missing sampleNames

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  2e30fc4

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• make sure EM counts are labeled as such

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  0fd3f9e

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• undo EM counts naming

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• name sampleData with prefix

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Commits on Sep 20, 2024

• catch error when 0 or 1 genes have counts

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Commits on Oct 4, 2024

• pass fusionmode to contruct read classes

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  e9ecc7b

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Commits on Oct 21, 2024

• Dont filter out reads that align up to the last nucleotide - fusions

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Commits on Oct 25, 2024

• Now will only combine SE read classes if min.txScore.singleExon < 1

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  d181c8e

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• Merge branch 'remov_SE_combineAnno' into Multiplex_Major_Patch

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  fa1a758

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• Merge branch 'full_NDR_output' into Multiplex_Major_Patch

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  b829e03

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• Update release history

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  77cae13

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• Merge branch 'messyForest' into Multiplex_Major_Patch

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Commits on Oct 28, 2024

• Fix merge

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• Refactor quantData input parameter and colData when not multiplexed

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  e133c43

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• update actions versions

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• Merge remote-tracking branch 'origin/Multiplex_Major_Patch' into Multiplex_Major_Patch

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  2b08636

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• Restore seperateSamples argument in writeBambuOutput lost in merge

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• Put gtf file extension at the end of writeBambuOutput

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• Add the flags in writeBambuOutput to control which gtfs are written

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• Update release history

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Commits on Oct 29, 2024

• Update xgboost models and include code to redo it

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  38cb052

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• Update quant test data due to assigndist changes

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  c1ab8af

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• Update remaining test data

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• Update version message

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• Add in preset modes

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• remove commas

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  09dcb4d

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• Fix mode

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Commits on Nov 4, 2024

• Fix reccomendNDR

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Commits on Nov 5, 2024

• Fix quantification when running bulk

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  a605fe7

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• restore returnDistTable

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• Return default degbias to on

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Commits on Nov 11, 2024

• Restore trackreads

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• Add in descriptions for new arguments

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  5d0af93

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• Merge branch 'filter_barcodes' into Multiplex_Major_Patch

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  121a3c2

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• Clean up cluster discovery

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  0b455ef

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Commits on Nov 22, 2024

• Fix issue with lowMem and multiple samples

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Commits on Dec 4, 2024

• Fix formatting in docu

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Commits on Dec 5, 2024

• returnDistTable now works when quant = TRUE

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• max recommended NDR is now 0.999

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• Return rcOutDir functionality

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• return distTable now returns intermediate distTable

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Commits on Dec 16, 2024

• lowMemory now processByBam and processByChromosome

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• Add lowMemory replacements to documentation and importBambuResults

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Commits on Dec 24, 2024

• Add more single cell documentation to readme

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Commits on Jan 2, 2025

• Fix bugs due to fusion mode on test data

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Commits on Jan 9, 2025

• fix library load warnings related to unname and expand function

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• bug fix for 0 value quantification

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• remove print line

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Commits on Jan 14, 2025

• min.txScore.singleExon bug fix

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Commits on Jan 15, 2025

• Merge pull request #456 from GoekeLab/singleExon_2

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  SuiYue-2308

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Commits on Jan 20, 2025

• fix barcodesToFilter not working bug

  cying111

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• fix typo in main function

  cying111

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• add documentation for barcodesToFilter argument and update the formats for some paragraphs

  cying111

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Commits on Jan 21, 2025

• add check flag when read name does not contain BC and UMI information

  cying111

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• comment unused code after return in generateUniqueCounts function

  cying111

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• comment out some internal messages to avoid duplicated output for each sample

  cying111

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  4f3c629

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• fix bug for demultiplexed when demultiplexed is provided as a file

  cying111

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• code style updates

  cying111

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• allow reads be NULL when quantData is provided for quant mode only

  cying111

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• fix typo

  cying111

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Commits on Jan 22, 2025

• update documentation

  cying111

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• add comment message to understand codes better

  cying111

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• update code style

  cying111

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Commits on Jan 23, 2025

• fix bug when clusters is provided as CharacterList produced as recommended in readme

  cying111

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  3d645e1

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• fix bug for reading in spatial files

  cying111

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  f25f2d3

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• fix the problem of not using unspliced SEs in default settings when min.txScore.singleExon == 1

  cying111

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• update function documentation

  cying111

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• update example code for clustercells with bug fix and update advanced option paper link

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Commits on Jan 24, 2025

• Merge pull request #458 from GoekeLab/Multiplex_Major_Patch

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Commits on Jan 26, 2025

• rename unused argument

  lingminhao

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Commits on Jan 27, 2025

• remove prefix "extended_annotations"

  SuiYue-2308

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• remove the basename(file) in writeToGTF

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Commits on Jan 28, 2025

• improve flexibility for BC&UMI parsing

  lingminhao

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Commits on Feb 3, 2025

• Add "_" after prefix

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• fix writeBambuOutpur error when this is no novel transcript in se object

  SuiYue-2308

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• fix importBambuResults

  SuiYue-2308

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• fix prefixes pass

  SuiYue-2308

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  0e673e4

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• fix the ifelse for novel Tx

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  2371bd6

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• fix importBambuResult when prefixes = ""

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• remove "}"

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  1cdf932

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Commits on Feb 5, 2025

• fix bug about CompressedCharacterList

  lingminhao

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  b122513

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Commits on Feb 6, 2025

• fix bug about CompressedCharacterList

  lingminhao

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  e316ebe

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Commits on Feb 7, 2025

• fix bug when cleanReads = T

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Commits on Feb 10, 2025

• change demultiplexed in mode

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• remove }

  SuiYue-2308

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  5762910

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Commits on Feb 11, 2025

• remove checking demultiplexed

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Commits on Feb 17, 2025

• Merge pull request #460 from GoekeLab/singleExon_2

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• fix rc assignment bug (multi-sample bambu-sc)

  lingminhao

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  4725911

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• fix rc assignment bug (multi-sample bambu-sc)

  lingminhao

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  69d2bf8

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Commits on Feb 28, 2025

• fix bug about CompressedCharacterList (revert)

  lingminhao

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  43baac1

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