Comments (1)
BarryDigby
commented on August 19, 2024
DEA.R will now produce:
A_vs_B, A_vs_C A_vs_D
B_vs_A, B_vs_C, B_vs_D
C_vs_A, C_vs_B, C_vs_D
D_vs_A, D_vs_B, D_vs_C
This produces duplicated outputs, but is extremely comprehensive and should be of use for those less familiar with the concepts of Fold Change direction. Changes implemented in BarryDigby/circrna, currently undergoing testing on minimal test-dataset.
Checklist:
- Ensure code works on test-dataset.
- Output
DESeq2results to unique contrast directory - Remove
main.nfphenotype check that assesses ifcontrolis present in the metadata file. - Update the documentation accordingly.
Pull request #27
from circrna.
Related Issues (20)
- Problems with scripts referenced using the ${workflow.projectDir} variable HOT 1
- Add support for RNAse-R effect correction
- [nf-core/circrna] error: Your FASTQ files do not have the appropriate extension HOT 19
- pipeline won't start without filling ref-genome bwa, bowtie, etc... HOT 2
- old version of /opt/conda/envs HOT 1
- Test workflow not working HOT 2
- Release Preparation Checklist HOT 1
- DSL2 modules HOT 1
- conda recepies HOT 8
- Not a valid path value: 'null' HOT 1
- Wrong BWA index directory in references HOT 7
- Issues generating, and pointing to, genome reference data lead to early crashes during configuration (w/ fix(?)) HOT 3
- Not all samples are used in analysis resulting in pipeline failur HOT 7
- Problem in running circrna HOT 2
- Limitted input length. HOT 2
- STAR, CIRIquant, DCC errors during pipeline run HOT 5
- Fix problems with outdated STAR indices in iGenomes HOT 1
- Implement coding potential analysis
- mapsplice error when input fasta file contains multiple fields in the header
- Implement improved annotation of hits also in the DIFFERENTIAL_EXPRESSION:PARENT_GENE process HOT 1
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from circrna.