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alyssafrazee
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polyester
Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
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fixed bug wrt strand specific simulation
#34
mikelove
closed
8 years ago
6
Sample-specific fragment GC bias and other changes
#33
mikelove
closed
8 years ago
1
Parallelize simulate_experiment()?
#32
kcha
opened
8 years ago
0
Bugfix
#31
alyssafrazee
closed
8 years ago
0
Move saving of coverage_matrices to proper code block.
#30
roryk
closed
8 years ago
1
Simulate 1 million reads at a time to avoid running out of memory.
#29
roryk
closed
8 years ago
18
simulate_experiment cannot handle 0 counts in transcripts
#28
roryk
opened
8 years ago
2
Distribution of reads
#27
shrukane
closed
8 years ago
6
Update simulate_experiment.Rd
#26
mikelove
closed
8 years ago
0
add info re: streaming quantifiers
#25
mikelove
closed
8 years ago
2
Error in seq_gtf(gtf, seqpath, ...) : unused argument (readlen = 70)
#24
irenerodriguez
opened
9 years ago
6
simulate_experminent crashes
#23
FabianGrammes
closed
9 years ago
1
output: .fasta.gz
#22
FabianGrammes
closed
9 years ago
2
Error with running simulate experiment for real human transcriptome
#21
vd4mmind
closed
3 years ago
11
Error in simulate_experiment
#20
qingl0331
closed
9 years ago
4
Update polyester.Rmd
#19
mikelove
closed
9 years ago
3
Math error with logmus of meanmodel
#18
warrenmcg
closed
9 years ago
2
Gene level expression
#17
johnmu
closed
9 years ago
1
compressed files
#16
shrukane
closed
9 years ago
1
Generating zero counts
#15
pimentel
closed
9 years ago
1
NB() not exported
#14
lcolladotor
closed
9 years ago
0
Stranded RNA-Seq
#13
jwcasement
closed
8 years ago
5
Instructions to install: not (yet) in bioconductor ?
#12
lgautier
closed
9 years ago
1
optimize parameter checks
#11
alyssafrazee
opened
10 years ago
0
keep read information
#10
alyssafrazee
opened
10 years ago
1
raise upper limit on number of nucleotides that can be in simulated sample
#9
alyssafrazee
closed
8 years ago
5
Invalid 'times' argument error while running simulate_experiment
#8
ersgupta
closed
10 years ago
4
made create_read_counts faster and less redundant
#7
jtleek
closed
10 years ago
0
read starting position and CIGAR
#6
esterpantaleo
opened
10 years ago
3
Update README.md
#5
mdshw5
closed
10 years ago
1
I added .gitignore which we'll take out when we submit to Bioc. I also allowed baseline simulation in generate_read_numbers
#4
jtleek
closed
10 years ago
0
typically, dispersion = 1 / size
#3
mikelove
closed
10 years ago
4
Usage examples in vignette
#2
stephenturner
closed
9 years ago
4
jeff's functions/moving vignette
#1
jtleek
closed
10 years ago
0
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