christophertbrown iRep issues

christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation

MIT License

68 stars 9 forks source link

issues

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Error with import and looking for advice for batch calculation

#43 ZeWLi opened 1 year ago
0
potential issue with np.arange(100,1000,10000) bPTR line 223

#42 mariaelf97 opened 1 year ago
0
Difficulties when using iRep with long read data

#41 mshamash opened 1 year ago
1
double free or corruption (!prev): 0x000055fa0a924e80 ***

#40 mariaelf97 closed 1 year ago
0
iRep requires

#39 maocheng2020 closed 2 years ago
5
A irep figure from my sample

#38 Anqi-Dai closed 2 years ago
7
Using GC Skew to reorder contigs

#37 balags1 opened 3 years ago
1
GC_skew for calculating bPTR and a bPTR value less than 1 or is NA

#36 Anqi-Dai closed 2 years ago
1
how different the rep rates need to be to be considered as such?

#35 xvazquezc opened 3 years ago
2
Enquiry on application of IREP to my experiments

#34 samkjm opened 3 years ago
1
super low GC bias in many samples results in n/a iRep values

#33 willnotburn opened 4 years ago
1
iRep and bPTR values lower than one

#32 yilmazbah closed 4 years ago
2
Different result if I use sorted SAM file as an input or use the unsorted SAM file as an input

#31 shashankx closed 4 years ago
4
iRep for long reads

#30 mdrishti closed 5 years ago
1
Multiple Sample for bPTR

#29 santoshe1 opened 5 years ago
1
Versions on Pypi broken

#28 epruesse opened 5 years ago
0
Anomalous iRep values

#27 stefcamp opened 5 years ago
0
Error thrown by parse_genomes_fa

#26 defleury opened 5 years ago
1
Update README.md: -s is required in example

#25 nr0cinu closed 4 years ago
1
iRep_filter.py overwrites coverage table with relative abundance table when run twice

#24 nr0cinu opened 5 years ago
1
bPTR output shows no coverage and calculated PTR

#23 sv1714 closed 5 years ago
3
choice of aligner?

#22 tamburinif closed 6 years ago
2
Gene-based binning

#21 annekup opened 6 years ago
3
iRep bias for lower coverage data

#20 lch14forever opened 6 years ago
1
iRep for origin of replication

#19 sarah872 opened 6 years ago
1
bPTR - ImportError for 'iRep.gc_skew'

#18 gerners closed 6 years ago
2
Add Python 3 as requirement in README.md

#17 hhollandmoritz closed 6 years ago
2
Error running sample dataset

#16 Anto007 closed 6 years ago
2
Remove outlier windows

#15 wrshoemaker closed 6 years ago
5
Bug fix about import fault from command line

#14 suzuki-shm closed 6 years ago
1
No results, numpy RuntimeWarning

#13 wrshoemaker closed 6 years ago
7
Syntax issues with python

#12 shaman-narayanasamy closed 6 years ago
6
problem in getting the right sam file

#11 AfredComma closed 6 years ago
1
problem in getting the PTR value

#10 liyun831229 closed 6 years ago
1
error with GC_skew

#9 BJCampbelllab closed 6 years ago
3
Stb support

#8 MrOlm closed 7 years ago
0
Restructure parsing

#7 MrOlm closed 7 years ago
0
added testing

#6 MrOlm closed 7 years ago
0
Confidence intervals on iRep estimation

#5 rprops opened 7 years ago
0
cPickle

#4 mocat2 closed 7 years ago
1
iRep/matplotlib crashes without X

#3 nr0cinu closed 7 years ago
2
sam files with spaces in sequence IDs

#2 ianpgm closed 7 years ago
1
threads and large files

#1 jbird9 opened 8 years ago
14