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theislab
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mubind
Learning motif contributions to cell transitions using sequence features and graphs.
https://mubind.readthedocs.io
MIT License
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n_sample_cells & n_sample_peaks
#137
shunyasanuma
closed
1 week ago
1
Generating atac.h5ad
#136
shunyasanuma
closed
3 weeks ago
3
3.9-3.12 testing.
#135
ilibarra
closed
1 month ago
0
AttributeError: 'csc_matrix' object has no attribute 'A'
#134
shunyasanuma
closed
1 month ago
3
Improve documentation of pancreas multiome dataset
#133
MUCDK
closed
1 week ago
2
Data downloading URL, actions, and dependencies.
#132
ilibarra
closed
1 month ago
1
Data Availability | Tutorial
#131
shunyasanuma
closed
3 weeks ago
15
Pancreas_atac h5ad object can't be downloaded
#130
xfchen0912
closed
1 month ago
5
fixes for release
#129
ilibarra
closed
1 month ago
1
Dev graph features
#128
ilibarra
closed
2 months ago
1
Error when running test_fit_model_knn_graph.py on GPU
#127
anna-lito
closed
2 months ago
2
Update README.md
#126
ilibarra
closed
1 year ago
0
Syntax
#125
ilibarra
closed
1 year ago
1
fixes to test
#124
ilibarra
closed
1 year ago
1
Scatac dynamic
#123
ilibarra
closed
1 year ago
1
tutorials for additional datasets missing
#122
ilibarra
opened
1 year ago
0
fixing dynamical calculation step using sparse matrices
#121
ilibarra
opened
1 year ago
0
inspection of counts in scATAC seq object
#120
ilibarra
opened
1 year ago
0
Move core notebooks to docs/notebooks
#119
ilibarra
opened
1 year ago
0
Sparsity module
#118
ilibarra
opened
1 year ago
0
NaNs for CTCF and other multibatch cases when number of rounds is one
#117
ilibarra
opened
1 year ago
0
Test that compare CPU/GPU speeds needed
#116
ilibarra
opened
1 year ago
0
training using I/O for large datasets.
#115
ilibarra
opened
1 year ago
0
Test for ChIP-seq processed data from bindome..
#114
ilibarra
opened
1 year ago
0
Calculation of relationships between related filters using distances graph
#113
ilibarra
opened
1 year ago
0
test_aggregate raises errors
#112
ilibarra
opened
1 year ago
0
addition of connectivity graph and activities as mulsum when dynamical system provided
#111
ilibarra
opened
1 year ago
0
Explore GRNN for atomic representations of protein sequences (instead of LSTMs).
#110
ilibarra
opened
1 year ago
0
Test for GenomicsDataset + optimize_iterative needed
#109
ilibarra
opened
1 year ago
0
binding_modes_to_multibind implementation
#108
ege-erdogan
closed
1 year ago
0
atomic DNA/protein multi-hot encodings
#107
ilibarra
opened
1 year ago
0
addition of MultiBindStackConv2D class and addition to pipeline.
#106
ilibarra
opened
1 year ago
0
renaming/refactoring of optimize_iterative/optimize function into model.MultiBind
#105
ilibarra
opened
1 year ago
0
model aggregation implementation & test
#104
ege-erdogan
closed
1 year ago
1
Addition of positional bias term
#103
ilibarra
opened
1 year ago
1
aggregation of filters/activities/etas into unified MultiBind instance
#102
ilibarra
opened
1 year ago
6
Additional conv_di representations
#101
ilibarra
opened
1 year ago
0
matmul in one-step instead of per batch in ActivitiesLayer forward
#100
ilibarra
closed
1 year ago
3
Triangular lower heatmap for dinucleotide features, below the mononucleotide features.
#99
ilibarra
closed
1 year ago
1
Dataset tests
#98
ege-erdogan
closed
1 year ago
1
Include flag in SelexDataset to use sparse counts instead of non-sparse counts (default)
#97
ilibarra
opened
1 year ago
1
Tests and functionality for sequences as integers
#96
ilibarra
closed
1 year ago
1
Use models.multibind instead of models.selexDataset in mubind-pipeline and make tests in mubind
#95
ilibarra
opened
1 year ago
6
remove comments
#94
ilibarra
closed
1 year ago
0
Conditions and tests for multi-batch modeling
#93
ilibarra
closed
1 year ago
0
Faster training / plotting with more coefficients and variable units for xlab/ylab.
#92
ilibarra
closed
1 year ago
1
optional r2_per epoch
#91
ilibarra
closed
1 year ago
0
Test fixes
#90
ilibarra
closed
1 year ago
1
Fixes in code / module renaming
#89
ilibarra
closed
1 year ago
0
Merge branch 'development' to 'main'
#88
ege-erdogan
closed
1 year ago
1
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