BIMSB bioinformatics platform / Akalin Lab janggu Issues

BIMSBbioinfo/janggu Issues

Compatibility with Biopython
Updated 5 months ago
GenomicIndexer Functionality
Closed 2 years ago2
keras.engine.topology
Closed 3 years ago19
Conflict between Numpy 1.19 and Keras
Updated 2 years ago
AxisError: axis 2 is out of bounds for array of dimension 2
Closed 3 years ago3
Index Error: tuple index out of range
Closed 3 years ago4
NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.
Closed 3 years ago3
Type Error: __init__() got an unexpected keyword argument 'epochs'
Closed 3 years ago1
"intersectBed" does not appear to be installed or on the path.
Closed 3 years ago3
NotImplementedError: "intersectBed" does not appear to be installed
Closed 3 years ago2
NameError :
Closed 3 years ago2
syntax Error:
Closed 3 years ago2
NotFoundError : _ZN10tensorflow8OpKernel11TraceStringB5cxx11EPNS_15OpKernelContextEb
Closed 3 years ago3
UnboundLocalError: local variable 'process_chrom' referenced before assignment
Closed 3 years ago2
String decoding error when running the CAGE prediction example
Closed 3 years ago3
BEDTools Installation
Closed 3 years ago7
Classify_nucleotide_sequences
Closed 4 years ago1
input_attribution from a Bioseq object
Closed 4 years ago4
Weird one-hot encode from sequences stored as biopython SeqRecord
Closed 4 years ago2
VariantStreamer fails if ROI is supplied when loading the reference genome
Closed 4 years ago2
Invalid interval bounds when creating from bigwig
Closed 4 years ago3
Compatibility with keras >=2.30 and tensorflow 2
Closed 4 years ago2
Problem with plotGenomeTrack
Closed 5 years ago2
flank-option close to chromosome boundaries leads to invalid genomic intervals, which can't be parsed correctly by utils._str_to_iv
Closed 5 years ago1
README
Closed 6 years ago2
Share datasets via browser cache in the Dash app
Closed 6 years ago1
BAM support for single-cell data
Closed 6 years ago1
[Model comparison] Add filtering options
Closed 6 years ago
BAM readout for paired-end datasets
Closed 6 years ago
Support for sparse datasets
Closed 6 years ago1

BIMSBbioinfo / janggu

BIMSBbioinfo/janggu Issues

Compatibility with Biopython

GenomicIndexer Functionality

keras.engine.topology

Conflict between Numpy 1.19 and Keras

AxisError: axis 2 is out of bounds for array of dimension 2

Index Error: tuple index out of range

NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.

Type Error: init() got an unexpected keyword argument 'epochs'

"intersectBed" does not appear to be installed or on the path.

NotImplementedError: "intersectBed" does not appear to be installed

NameError :

syntax Error:

NotFoundError : _ZN10tensorflow8OpKernel11TraceStringB5cxx11EPNS_15OpKernelContextEb

UnboundLocalError: local variable 'process_chrom' referenced before assignment

String decoding error when running the CAGE prediction example

BEDTools Installation

Classify_nucleotide_sequences

input_attribution from a Bioseq object

Weird one-hot encode from sequences stored as biopython SeqRecord

VariantStreamer fails if ROI is supplied when loading the reference genome

Invalid interval bounds when creating from bigwig

Compatibility with keras >=2.30 and tensorflow 2

Problem with plotGenomeTrack

flank-option close to chromosome boundaries leads to invalid genomic intervals, which can't be parsed correctly by utils._str_to_iv

README

Share datasets via browser cache in the Dash app

BAM support for single-cell data

[Model comparison] Add filtering options

BAM readout for paired-end datasets

Support for sparse datasets