.gitignore
README.md
environment.yaml
setup.py
figures/Xenomake Workflow.png
figures/config.png
figures/human_mouse_split.jpg
figures/scanpy_qc.png
xenomake/__init__.py
xenomake/config.py
xenomake/errors.py
xenomake/smk.py
xenomake/utils.py
xenomake.egg-info/PKG-INFO
xenomake.egg-info/SOURCES.txt
xenomake.egg-info/dependency_links.txt
xenomake.egg-info/entry_points.txt
xenomake.egg-info/requires.txt
xenomake.egg-info/top_level.txt
xenomake/data/config_structure.yaml
xenomake/data/defaults_runmode.yaml
xenomake/data/defaults_spatmode.yaml
xenomake/data/picard.jar
xenomake/data/Drop-seq_tools-2.5.3/AssignCellsToSamples
xenomake/data/Drop-seq_tools-2.5.3/BamTagHistogram
xenomake/data/Drop-seq_tools-2.5.3/BamTagOfTagCounts
xenomake/data/Drop-seq_tools-2.5.3/BaseDistributionAtReadPosition
xenomake/data/Drop-seq_tools-2.5.3/BipartiteRabiesVirusCollapse
xenomake/data/Drop-seq_tools-2.5.3/CensusSeq
xenomake/data/Drop-seq_tools-2.5.3/CollapseBarcodesInPlace
xenomake/data/Drop-seq_tools-2.5.3/CollapseTagWithContext
xenomake/data/Drop-seq_tools-2.5.3/CompareDropSeqAlignments
xenomake/data/Drop-seq_tools-2.5.3/ComputeUMISharing
xenomake/data/Drop-seq_tools-2.5.3/ConvertTagToReadGroup
xenomake/data/Drop-seq_tools-2.5.3/ConvertToRefFlat
xenomake/data/Drop-seq_tools-2.5.3/CountUnmatchedSampleIndices
xenomake/data/Drop-seq_tools-2.5.3/CreateIntervalsFiles
xenomake/data/Drop-seq_tools-2.5.3/CreateMetaCells
xenomake/data/Drop-seq_tools-2.5.3/CreateSnpIntervalFromVcf
xenomake/data/Drop-seq_tools-2.5.3/CsiAnalysis
xenomake/data/Drop-seq_tools-2.5.3/DetectBeadSubstitutionErrors
xenomake/data/Drop-seq_tools-2.5.3/DetectBeadSynthesisErrors
xenomake/data/Drop-seq_tools-2.5.3/DetectDoublets
xenomake/data/Drop-seq_tools-2.5.3/DigitalExpression
xenomake/data/Drop-seq_tools-2.5.3/DownsampleBamByTag
xenomake/data/Drop-seq_tools-2.5.3/DownsampleTranscriptsAndQuantiles
xenomake/data/Drop-seq_tools-2.5.3/Drop-seq_Alignment_Cookbook.pdf
xenomake/data/Drop-seq_tools-2.5.3/Drop-seq_alignment.sh
xenomake/data/Drop-seq_tools-2.5.3/FilterBam
xenomake/data/Drop-seq_tools-2.5.3/FilterBamByGeneFunction
xenomake/data/Drop-seq_tools-2.5.3/FilterBamByTag
xenomake/data/Drop-seq_tools-2.5.3/FilterDge
xenomake/data/Drop-seq_tools-2.5.3/FilterGtf
xenomake/data/Drop-seq_tools-2.5.3/FilterValidRabiesBarcodes
xenomake/data/Drop-seq_tools-2.5.3/GatherGeneGCLength
xenomake/data/Drop-seq_tools-2.5.3/GatherMolecularBarcodeDistributionByGene
xenomake/data/Drop-seq_tools-2.5.3/GatherReadQualityMetrics
xenomake/data/Drop-seq_tools-2.5.3/GenotypeSperm
xenomake/data/Drop-seq_tools-2.5.3/MarkChimericReads
xenomake/data/Drop-seq_tools-2.5.3/MaskReferenceSequence
xenomake/data/Drop-seq_tools-2.5.3/MergeDgeSparse
xenomake/data/Drop-seq_tools-2.5.3/PolyATrimmer
xenomake/data/Drop-seq_tools-2.5.3/ReduceGtf
xenomake/data/Drop-seq_tools-2.5.3/RollCall
xenomake/data/Drop-seq_tools-2.5.3/SelectCellsByNumTranscripts
xenomake/data/Drop-seq_tools-2.5.3/SignTest
xenomake/data/Drop-seq_tools-2.5.3/SingleCellRnaSeqMetricsCollector
xenomake/data/Drop-seq_tools-2.5.3/SpermSeqMarkDuplicates
xenomake/data/Drop-seq_tools-2.5.3/SplitBamByCell
xenomake/data/Drop-seq_tools-2.5.3/TagBam
xenomake/data/Drop-seq_tools-2.5.3/TagBamWithReadSequenceExtended
xenomake/data/Drop-seq_tools-2.5.3/TagReadWithGeneExonFunction
xenomake/data/Drop-seq_tools-2.5.3/TagReadWithGeneFunction
xenomake/data/Drop-seq_tools-2.5.3/TagReadWithInterval
xenomake/data/Drop-seq_tools-2.5.3/TagReadWithRabiesBarcodes
xenomake/data/Drop-seq_tools-2.5.3/TrimStartingSequence
xenomake/data/Drop-seq_tools-2.5.3/ValidateAlignedSam
xenomake/data/Drop-seq_tools-2.5.3/ValidateReference
xenomake/data/Drop-seq_tools-2.5.3/create_Drop-seq_reference_metadata.sh
xenomake/data/Drop-seq_tools-2.5.3/loadDotKits.sh
xenomake/data/Drop-seq_tools-2.5.3/3rdParty/picard/picard.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/dropseq.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/biojava-alignment-6.0.3.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/biojava-core-6.0.3.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/commons-collections4-4.0-alpha1.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/commons-lang-2.5.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/guava-22.0.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/jdistlib-0.4.4-bin.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/la4j-0.5.5.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/picard-2.26.10.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/slf4j-api-1.7.32.jar
xenomake/data/Drop-seq_tools-2.5.3/jar/lib/snakeyaml-1.17.jar
xenomake/data/barcodes/3M-february-2018.txt.gz
xenomake/data/barcodes/737K-fixed-rna-profiling.txt
xenomake/data/barcodes/dbit-seq_barcode_positions.csv
xenomake/data/barcodes/dbit_seq_barcodes.txt
xenomake/data/barcodes/visium_barcode_positions.csv
xenomake/data/barcodes/visium_barcodes.txt
xenomake/data/urls/human_index_urls.txt
xenomake/data/urls/mouse_index_urls.txt
xenomake/data/urls/species_urls.txt
xenomake/data/urls/xengsort_index_urls.txt
xenomake/postprocess/Downstream.py
xenomake/postprocess/convert_long.py
xenomake/postprocess/create_hdf5.py
xenomake/postprocess/make_h5ad.py
xenomake/postprocess/qc.py
xenomake/postprocess/spatial_barcode.py
xenomake/scripts/clean_top_barcodes.py
xenomake/scripts/commands.sh
xenomake/scripts/extract_seqscope_coordinates.sh
xenomake/scripts/filter_mm_reads.py
xenomake/scripts/filter_mm_reads_both.py
xenomake/scripts/find_overlapped_reads.py
xenomake/scripts/fix_bam_headers.py
xenomake/scripts/gtf_parse.sh
xenomake/scripts/overlapped_reads.py
xenomake/scripts/reformat.pl
xenomake/scripts/splice_bam_header.py
xenomake/scripts/tag_reads.py
xenomake/scripts/trim_sequence.py
xenomake/snakemake/annData.smk
xenomake/snakemake/expression.smk
xenomake/snakemake/main.smk
xenomake/snakemake/mapping.smk
xenomake/snakemake/multimapped.smk
xenomake/snakemake/qc.smk
xenomake/snakemake/reformat.py
xenomake/snakemake/xengsort.smk