alyssafrazee polyester issues

alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.

http://biorxiv.org/content/early/2014/12/12/006015

90 stars 51 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Snakemake workflow of Polyester

#84 NaotoKubota closed 3 months ago
1
Question about run time length

#83 cmill221 opened 1 year ago
0
Simulating Fastq files

#82 TdzBAS closed 1 year ago
1
Exact number for reads_per_transcript simulated reads

#81 Glenn032787 opened 2 years ago
0
simulate_experiment discrepancy in basemean values for simulated data

#80 vavouri-lab opened 2 years ago
0
Specifying Number of Reads Overall

#79 nmshahir opened 2 years ago
0
Simulate Reads Without Experiment?

#78 nmshahir closed 2 years ago
3
Simulation of error-free reads

#77 hl-xue opened 3 years ago
0
Support for GFF3

#76 TBooker opened 3 years ago
1
Fixing non-deterministic behavior when seed is set and meanmodel logic

#75 NatPRoach closed 3 years ago
1
Error when report_coverage is set to true

#74 NatPRoach closed 3 years ago
1
fix fraglen error: negative values are not allowed in width

#73 scottlallen closed 3 years ago
0
Typo in the documentation re fold_changes in simulate_experiment

#72 ning-y opened 4 years ago
0
error in function simulate_experiment_countmat

#71 mhjiang97 opened 4 years ago
0
make output of create_read_numbers traceable to input values

#70 stu2 closed 3 years ago
1
Wrong transcript on negative strand when using gtf and genome files

#69 quirinmanz closed 4 years ago
2
simulate_experiment() fails when idfield (default: "transcript_id") is not present in the first line of the gtf file

#68 alorchhota opened 5 years ago
0
GCbias discrepancy

#67 Glfrey opened 5 years ago
0
A few suggestions

#66 sagnikbanerjee15 opened 5 years ago
0
Invalid 'times' argument after simulate_experiment - works with subsetted dataset

#65 orangebromeliad closed 5 years ago
2
Only outputting one file?

#64 theheking opened 5 years ago
5
Read length longer than 100 with illumina4 platform error

#63 tonyyzy opened 5 years ago
0
basemeans in simulate_experiment when num_rep == 1

#62 orangebromeliad opened 5 years ago
2
Simulated strand-specific reads were weird

#61 yh549848 closed 5 years ago
2
customizing positional and GC biases

#60 Congm12 opened 6 years ago
3
fix bug on readlen

#59 ghost closed 3 years ago
2
Fixed typo in vignette

#58 jakejh closed 6 years ago
2
Shuffle Option, Add Error Info, & Speedups Part 2

#57 warrenmcg closed 3 years ago
6
Fix to mate2 name creation in generate_fragments.R

#56 silva1jos closed 3 years ago
0
gcbias argument in simulate experiment

#55 Aslic opened 6 years ago
1
Output of FASTQ or QUAL in addtion to FASTA

#54 medcelerate opened 6 years ago
1
Which bases are mutated?

#53 SaraEl-Metwally closed 6 years ago
0
[feature request] Explicitly label mutated bases in simulated reads.

#52 SaraEl-Metwally opened 6 years ago
1
bugfix - avoids duplicated read IDs

#51 vllorens closed 6 years ago
2
Duplicated read IDs using simulate_experiment_countmat()

#50 vllorens opened 6 years ago
1
Keep reads_per_transcript positive

#49 mourisl closed 6 years ago
3
simulate_experiment failing with 2 column fold_changes matrix...

#48 nickschurch closed 7 years ago
3
simulate_experiment cannot handle 0 counts in transcripts [DUPLICATE]

#47 aarzalluz closed 7 years ago
0
Basemeans uninitialized in case num_reps == 1

#46 duyck closed 7 years ago
2
fix input validation for gcbias

#45 javiljoen closed 7 years ago
1
`simulate_experiment` does not accept a list of numerics for `gcbias`

#44 javiljoen closed 7 years ago
2
Problems with matrix while running the simulate experiment

#43 alessandraalves closed 7 years ago
4
basemeans: number of items to replace is not a multiple of replacement length

#42 mikelove closed 8 years ago
3
"negative length vectors are not allowed" ?

#41 ireneg closed 8 years ago
2
strand specific argument

#40 dn070017 opened 8 years ago
4
Matrices, son.

#39 alyssafrazee closed 8 years ago
1
Performance tweak

#38 ttdtrang closed 3 years ago
3
Trouble changing size parameter

#37 rramaker opened 8 years ago
5
Time and memore requirements

#36 mw55309 opened 8 years ago
3
Error in as.matrix(basemeans)[, group_id] : subscript out of bounds (simulate_experiment)

#35 mw55309 closed 8 years ago
2