lweasel piquant issues - Githubissues

lweasel / piquant

A pipeline to assess the quantification of transcripts.

http://piquant.readthedocs.org/en/latest/

MIT License

19 stars 4 forks source link

issues

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Bump numpy from 1.10.4 to 1.21.0

#65 dependabot[bot] closed 2 years ago
0
Bump py from 1.4.20 to 1.10.0

#64 dependabot[bot] closed 2 years ago
0
Bump pygments from 1.6 to 2.7.4

#63 dependabot[bot] closed 2 years ago
0
Add threshold for short transcripts

#62 lweasel opened 7 years ago
0
Mention samtools version tested with in documentation

#61 lweasel opened 7 years ago
0
Prequantification fails if GTF attribute values contain spaces

#60 lweasel opened 7 years ago
0
Update ReadTheDocs URLs (.org -> .io)

#59 lweasel opened 8 years ago
0
Consider the effect of effective length correction (pun intended)

#58 rob-p opened 8 years ago
1
Allow relative paths for GTF files

#57 lweasel opened 8 years ago
0
Bias motif PWM file not copied to correct location during package installation

#56 lweasel closed 8 years ago
1
Clarify "Typical pipeline usage" documentation

#55 lweasel opened 8 years ago
0
Incorrect demand that "--noise_transcript_gtf" option be specified

#54 lweasel opened 8 years ago
0
Develop

#53 rob-p closed 9 years ago
2
Add units to plot axis labels

#52 lweasel closed 9 years ago
1
Randomise strand for "unstranded" paired-end reads

#51 lweasel closed 9 years ago
1
Feature Request: Record & report usage statistics for (pre-)quantification steps

#50 rob-p closed 9 years ago
6
Fixed some bugs related to analyse_runs

#49 rob-p closed 9 years ago
5
Add script/command description to usage messages

#48 lweasel closed 9 years ago
1
Check v1.1 changes under Python 3.4.

#47 lweasel closed 9 years ago
1
Misspelled parameters in params file are ignored

#46 lweasel closed 10 years ago
0
Prevent negative values of read length, depth etc.

#45 lweasel closed 9 years ago
1
Incorporate "read noise" as a quantification parameter

#44 lweasel closed 9 years ago
2
Incorporate strandedness of reads as quantification parameter

#43 lweasel closed 9 years ago
1
Make creation of output directories consistent

#42 lweasel closed 9 years ago
1
Update to latest version of quantification tools

#41 lweasel closed 9 years ago
1
Doc string typo prevents simulate_read_bias script operating

#40 lweasel closed 10 years ago
0
Finish first draft of documentation

#39 lweasel closed 10 years ago
1
Fixed typo in write_quantification_commands for Salmon

#38 rob-p closed 10 years ago
2
check_reads should check that the right number of reads were created.

#37 lweasel closed 10 years ago
0
Tidy writing of commands in prepare_read_simulation

#36 lweasel closed 10 years ago
0
Should be able to specify separate read and quantification parent directories

#35 lweasel closed 9 years ago
1
Implement gene-level accuracy analysis

#34 lweasel closed 9 years ago
1
Produce consistent set of plots for a single quantification run

#33 lweasel closed 10 years ago
0
Add option for graph output format

#32 lweasel closed 10 years ago
1
Race condition in prequantify step.

#31 lweasel closed 10 years ago
0
Fix error message for unknown quantification method

#30 lweasel closed 10 years ago
0
Make GROUPED_STATS_NUM_TPMS_FILTER user-definable via option

#29 lweasel closed 10 years ago
0
Define order for fixed parameter values in plot file names/titles

#28 lweasel closed 10 years ago
0
Make ERROR_PERCENTAGE_THRESHOLD a user-definable option

#27 lweasel closed 9 years ago
1
Make NOT_PRESENT_CUTOFF a user-definable option

#26 lweasel closed 9 years ago
1
Queries on contents of distribution stats files

#25 lweasel closed 10 years ago
0
Check piquant scripts work with Python 3

#24 lweasel closed 10 years ago
0
Move top-level scripts into scripts/ directory

#23 lweasel closed 10 years ago
2
Deal with ordutils dependency

#22 lweasel closed 10 years ago
1
Cleanup of non-essential files not working for RSEM

#21 lweasel closed 10 years ago
0
Remove strand-specific quantification options in single-end case

#20 lweasel closed 10 years ago
0
Remove --output-genome-bam option when running RSEM

#19 lweasel closed 10 years ago
0
Add piquant.py option to control no. of threads used by quantifiers etc.

#18 lweasel closed 9 years ago
1
Temporary read files should be deleted unless -nocleanup is set

#17 lweasel closed 10 years ago
1
Strandedness wrong for Cufflinks quantification

#16 lweasel closed 10 years ago
0