3DGenomes/TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
PythonGPL-3.0
Issues
- 1
Adding support for Spacewalk files in tadbit model
#393 opened by iagomaceda - 0
TAD calling weird behaviour
#392 opened by iagooteroc - 10
Restriction with Arima kit
#391 opened by jeff-godwin - 3
Error of TADbit clean
#389 opened by iagomaceda - 7
Tadbit Parse Error
#345 opened by eng3001 - 5
- 0
Error during parse_sam()
#387 opened by dnygard - 0
Export to .hic error
#386 opened by manuelfmerino - 3
tadbit map getting stuck
#385 opened by leomorelli - 0
loop_model.json file required to run loopbit
#384 opened by AAli-90 - 0
Error loading mcool file
#383 opened by ericmalekos - 0
Error in tadbit parse
#382 opened by iwbaek0828 - 3
TADbit bin not generating a symmetric matrix
#377 opened by pollicipes - 2
- 2
Mapping problem tutorial
#373 opened by manuelfmerino - 2
Matrix is too sparse after mapping
#374 opened by manuelfmerino - 1
Problem with building from Dockerfile
#372 opened by yann-zhong - 1
Tests fail
#371 opened by rekado - 3
Problem while modelling
#370 opened by AngieD9110 - 0
Parsing bam during ICE normalization
#365 opened by vntasis - 3
oneD normalization
#366 opened by alkurowska - 1
HIC matrix in .mat format
#363 opened by alkurowska - 5
any way from bowtie2 aligned bam file or filtered pairs file to the tadbit compatible bam file?
#295 opened by brainfo - 1
TADbit export error
#364 opened by alkurowska - 5
Problem with the weight values in cooler output
#359 opened by vntasis - 2
Incompatible cooler format
#358 opened by vntasis - 1
Issue in tutorial with fastq-dump -DQ option
#353 opened by ChristianKKelley - 1
Unknown error with process
#352 opened by poflawless - 2
- 1
gem-mappability
#351 opened by alkurowska - 1
pair-map using bowtie2 by --mapper failed
#348 opened by hao-yanan - 9
tadbit map ValueError
#344 opened by eng3001 - 9
model problem
#343 opened by Guoshuai1314 - 2
use TADbit on Capture Hi-C dataset
#342 opened by jazberna1 - 4
abnormal eigenvectors
#341 opened by shiyi-pan - 4
- 1
TADs numbers problem
#339 opened by shiyi-pan - 3
TADs calls problem
#338 opened by shiyi-pan - 2
gem tbz2 don't has the gem-mappability module
#337 opened by shiyi-pan - 0
Understanding write_interaction_pairs output
#334 opened by Biojenifer - 2
Bins to genomic coordinates
#328 opened by aalvarezf - 2
How to calculate the mapping rate?
#325 opened by CaiCheng1996 - 1
How to get the coordinates of TAD
#324 opened by CaiCheng1996 - 0
Keep only uniquely mapped reads pairs
#321 opened by CaiCheng1996 - 2
How to save the output ?
#322 opened by CaiCheng1996 - 2
Error in load chromosome
#320 opened by lauradmartens - 2
Error division by zero in find_compartments
#318 opened by apaytuvi - 2
Load .hic file for Compartments and TADs detection?
#316 opened by awezmm - 1
- 1
problem with installation
#289 opened by DonStephano