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28 Open 27 Closed
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Issues list

Question about run time length
#83 opened Apr 16, 2023 by cmill221
Exact number for reads_per_transcript simulated reads
#81 opened Aug 15, 2022 by Glenn032787
simulate_experiment discrepancy in basemean values for simulated data
#80 opened Jun 8, 2022 by vavouri-lab
Specifying Number of Reads Overall
#79 opened Dec 8, 2021 by nmshahir
Simulation of error-free reads
#77 opened Oct 6, 2021 by hl-xue
Support for GFF3
#76 opened Aug 27, 2021 by TBooker
1
Typo in the documentation re fold_changes in simulate_experiment
#72 opened Aug 23, 2020 by ning-y
error in function simulate_experiment_countmat
#71 opened Aug 12, 2020 by mhjiang97
simulate_experiment() fails when idfield (default: "transcript_id") is not present in the first line of the gtf file
#68 opened Oct 9, 2019 by alorchhota
GCbias discrepancy
#67 opened Aug 9, 2019 by Glfrey
A few suggestions
#66 opened Apr 3, 2019 by sagnikbanerjee15
Only outputting one file?
#64 opened Mar 24, 2019 by theheking
5
Read length longer than 100 with illumina4 platform error
#63 opened Mar 22, 2019 by tonyyzy
basemeans in simulate_experiment when num_rep == 1
#62 opened Mar 22, 2019 by orangebromeliad
2
customizing positional and GC biases
#60 opened Oct 1, 2018 by Congm12
3
gcbias argument in simulate experiment
#55 opened Apr 13, 2018 by Aslic
1
Output of FASTQ or QUAL in addtion to FASTA
#54 opened Mar 29, 2018 by medcelerate
1
[feature request] Explicitly label mutated bases in simulated reads.
#52 opened Jan 25, 2018 by SaraEl-Metwally
1
Duplicated read IDs using simulate_experiment_countmat()
#50 opened Jan 16, 2018 by vllorens
1
strand specific argument
#40 opened Sep 22, 2016 by dn070017
4
Trouble changing size parameter
#37 opened Sep 4, 2016 by rramaker
5
Time and memore requirements
#36 opened Aug 19, 2016 by mw55309
3
Parallelize simulate_experiment()?
#32 opened Feb 17, 2016 by kcha
simulate_experiment cannot handle 0 counts in transcripts
#28 opened Nov 4, 2015 by roryk
2
Error in seq_gtf(gtf, seqpath, ...) : unused argument (readlen = 70)
#24 opened Sep 23, 2015 by irenerodriguez
6
ProTip! What’s not been updated in a month: updated:<2024-06-20.