Comments (4)
grst
commented on July 18, 2024
In GitLab by @grst on Mar 20, 2020, 18:37
changed the description
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grst
commented on July 18, 2024
In GitLab by @grst on Apr 6, 2020, 17:15
changed the description
from scirpy.
grst
commented on July 18, 2024
In GitLab by @grst on Apr 7, 2020, 17:24
Include overview figure from the paper in README
Figure 1: The scirpy workflow. After defining clonotypes via CDR3-sequence similarity, scirpy offers a wide range of visualization options to explore clonotype expansion, abundance and VDJ gene usage. Finally, clonotype information can be integrated with transcriptomics data, leveraging the scanpy workflow. Top panel: Exemplary clonotype network. Each node represents a cell, colored by sample. Edges connect cells belonging to the same clonotype. Middle panel: Clonal expansion visualized as bar chart. The bars colored in blue, orange and green represent the fractions of cells belonging to clonotypes with one, two or more than two cells, respectively. Lower panel: UMAP embedding based on gene expression. Cells belonging to the twelve most abundant clonotypes are highlighted in color.
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grst
commented on July 18, 2024
All todos have been addressed in #124 or been migrated into their own issues.
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Related Issues (20)
- Cannot convert output from Scirpy to dandelion HOT 19
- airr validation fails when converting demo dataset to_airr_cells HOT 1
- minor bug? non-productive contigs appearing as productive and order of contigs HOT 5
- spatial airr data HOT 3
- Installation problem HOT 6
- error for computing nucleotide sequence identity using multiple samples HOT 2
- Error in loading filtered_contig_annotations.csv HOT 3
- does not merge correctly using merge_with_ir HOT 2
- ir.tl.clonotype_network() The function runs with "Aborted (core dumped)" error? HOT 2
- Speed up read_airr
- speed up define_clonotypes
- Autoencoder-based sequence embedding HOT 10
- Scalability to >1M cells
- antigen specificity prediction
- switch to cookiecutter-scverse template
- Anything to do about plt.subplot HOT 4
- clean up usage of _is_na, _is_true and _is_false
- Allow only high confidence filtering when reading Cell Ranger output HOT 6
- MuData API considerations HOT 2
- Split IO into separate package HOT 2
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