caravagnalab rRACES issues

caravagnalab / rRACES

R wrapper for the RACES package

GNU General Public License v3.0

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issues

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Sequencing per chromosome does not produce uniform coverage

#124 albertocasagrande closed 1 week ago
0
Naming

#123 caravagn opened 2 months ago
0
Error in plotting functions when more than 12 populations

#122 elena-buscaroli closed 2 months ago
0
`annotate_forest` function is not using the right exposure time

#121 vvvirgy opened 4 months ago
0
Conditioning on population surviving

#120 riccardobergamin opened 4 months ago
0
Problem with `m_engine$place_mutations`

#119 nicola-calonaci closed 2 months ago
1
Improvements `simulate_seq` function

#118 jovoni closed 1 week ago
4
plot_exposure_timeline function modification

#117 azadsadr closed 2 months ago
0
seed issue

#116 riccardobergamin closed 5 months ago
0
Error with get_samples_forest()

#115 Militeee closed 5 months ago
1
aborting session with this example

#114 riccardobergamin closed 5 months ago
2
Base quality of simulated reads is very low

#113 giorgiagandolfi closed 6 months ago
0
Evolutionary parameters getter function

#112 azadsadr closed 6 months ago
0
Simulate sequencing with Illumina error

#111 giorgiagandolfi closed 6 months ago
5
Cheatsheet errors/improvements

#110 albertocasagrande opened 6 months ago
2
Absolute coordinates for chromosomes

#109 jovoni closed 6 months ago
4
The documentation lacks info about indels

#108 albertocasagrande closed 6 months ago
0
`seq_to_long()` issue

#107 albertocasagrande closed 6 months ago
2
New version of ensembl references

#106 giorgiagandolfi closed 6 months ago
1
some issue with the sequencing

#105 riccardobergamin closed 7 months ago
1
forest$get_sticks

#104 riccardobergamin closed 6 months ago
0
installation issue

#103 riccardobergamin closed 7 months ago
2
forest$get_sticks provide empty list

#102 riccardobergamin closed 7 months ago
1
Error in building a MutationEngine even by using the "demo" setup

#101 saracoco closed 7 months ago
3
Functions not exported and wrong examples

#100 albertocasagrande closed 6 months ago
3
`simulate_seq` time speed-up

#99 valerianilucrezia closed 7 months ago
6
Wrong cell file format error

#97 jovoni closed 8 months ago
0
Germline sources for other chromosomes

#96 giorgiagandolfi closed 8 months ago
1
Sam validation error for paired reads

#95 giorgiagandolfi closed 8 months ago
1
`get_rates` and `update_rates` fail to get and update the epigenetic switching rates

#94 albertocasagrande closed 8 months ago
0
run_up_to_size

#93 caravagn closed 8 months ago
2
Many issues in `plot_exposure_time`

#92 albertocasagrande closed 8 months ago
0
Add SM tag in RG filed of simulated SAM files

#91 giorgiagandolfi closed 8 months ago
3
Write SAM file with set purity gives error

#90 giorgiagandolfi closed 8 months ago
0
Floating point exception(core dumped) error at sim$get_samples_forest

#89 riccardobergamin closed 6 months ago
13
Support Windows systems

#88 albertocasagrande closed 8 months ago
2
Re-building from scratch the mutation engine is required to observe CN events

#87 jovoni closed 8 months ago
0
Germline subject 2 has a strange mutation distribution

#86 valerianilucrezia closed 9 months ago
0
problem with muller plot

#85 riccardobergamin closed 8 months ago
2
RStudio session aborted when high number of cells are searched

#84 valerianilucrezia closed 8 months ago
6
strange error : "Wrong cell file format"

#83 riccardobergamin closed 8 months ago
5
The directory "/tmp/races_20240226-184547" already exists

#82 riccardobergamin closed 9 months ago
2
some issue with the sequencing

#81 riccardobergamin closed 8 months ago
12
karyotype column

#80 riccardobergamin closed 8 months ago
3
unkwown chromosome 6

#79 riccardobergamin closed 9 months ago
2
error with mutation engine loading on unix

#78 riccardobergamin closed 9 months ago
6
SNVS in sequencing does not match the ones in phylogenetic forest

#77 riccardobergamin closed 9 months ago
6
CTRL-C handing

#76 albertocasagrande opened 9 months ago
0
Simulated read error model

#75 albertocasagrande closed 8 months ago
3
Produce germline SAM file

#74 albertocasagrande closed 8 months ago
1