nf-core · OlivierCoen · May 17, 2025
diff --git a/README.md b/README.md
@@ -1,38 +1,8 @@
 # ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
-Test data to be used for automated testing with the nf-core pipelines
 
-> ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)**
+# test-datasets: stableexpression
+This branch contains test data to be used for automated testing with the nf-core/stableexpression pipeline.
 
-## Introduction
+## Content of this repository
 
-nf-core is a collection of high quality Nextflow pipelines. This repository contains various files for CI and unit testing of nf-core pipelines and infrastructure.
-
-The principle for nf-core test data is as small as possible, as large as necessary. Please see the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines) for more detailed information. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data.
-
-## Documentation
-
-nf-core/test-datasets comes with documentation in the `docs/` directory:
-
-01. [Add a new  test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
-02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
-
-## Downloading test data
-
-Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use.
-
-```bash
-git clone <url> --single-branch --branch <pipeline/modules/branch_name>
-```
-
-To subsequently clone other branches[^1]
-
-```bash
-git remote set-branches --add origin [remote-branch]
-git fetch
-```
-
-## Support
-
-For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging).
-
-[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856)
+All the data contained here were subsampled from datasets collected from Expression. In some cases, data were also generated randomly.
diff --git a/test_data/dataset_statistics/input/count.raw.cpm.quant_norm.parquet b/test_data/dataset_statistics/input/count.raw.cpm.quant_norm.parquet
diff --git a/test_data/gene_statistics/input/gene_counts.csv b/test_data/gene_statistics/input/gene_counts.csv
@@ -0,0 +1,28 @@
+sample,count
+ARR029909,4
+ARR029910,4
+ARR029911,4
+ARR029912,4
+ARR029913,4
+ARR029914,4
+ARR029915,4
+ARR029916,4
+ARR029917,4
+URR029909,2
+URR029910,2
+URR029911,2
+URR029912,2
+URR029913,2
+URR029914,2
+URR029915,2
+URR029916,2
+URR029917,2
+ERR029909,3
+ERR029910,3
+ERR029911,3
+ERR029912,3
+ERR029913,3
+ERR029914,3
+ERR029915,3
+ERR029916,3
+ERR029917,3
diff --git a/test_data/gene_statistics/input/ks_stats.csv b/test_data/gene_statistics/input/ks_stats.csv
@@ -0,0 +1,27 @@
+URR029909,0.99
+URR029910,0.58
+URR029911,0.24
+URR029912,0.12
+URR029913,0.05
+URR029914,0.0
+URR029915,0.897
+URR029916,0.999
+URR029917,0.23
+ERR029909,0.45
+ERR029910,0.87
+ERR029911,0.456
+ERR029912,0.457
+ERR029913,0.78
+ERR029914,0.32
+ERR029915,0.56
+ERR029916,0.45
+ERR029917,0.12
+ARR029909,0.21
+ARR029910,0.0000005
+ARR029911,0
+ARR029912,0.789
+ARR029913,0.987
+ARR029914,0.876
+ARR029915,0.123
+ARR029916,0.321
+ARR029917,0.156
diff --git a/test_data/gene_statistics/input/mapping1.csv b/test_data/gene_statistics/input/mapping1.csv
@@ -0,0 +1,9 @@
+original_gene_id,ensembl_gene_id
+Q8VWG3,AT1G34790
+Q9FJA2,AT5G35550
+Q8RYD9,AT5G23260
+ABCD12,AT5G23261
+840386,AT1G34790
+833520,AT5G35550
+832390,AT5G23260
+123456,AT5G35550
diff --git a/test_data/gene_statistics/input/mapping2.csv b/test_data/gene_statistics/input/mapping2.csv
@@ -0,0 +1,9 @@
+original_gene_id,ensembl_gene_id
+Q8VWG3,AT1G34790
+Q9FJA2,AT5G35550
+Q8RYD9,AT5G23260
+ABCD12,AT5G23261
+840386,AT1G34790
+833520,AT5G35550
+832390,AT5G23260
+457862,AT5G23260
diff --git a/test_data/gene_statistics/input/mapping3.csv b/test_data/gene_statistics/input/mapping3.csv
@@ -0,0 +1,5 @@
+original_gene_id,ensembl_gene_id
+Q8VWG3,AT1G34790
+Q9FJA2,AT5G35550
+Q8RYD9,AT5G23260
+152348,AT1G23260
diff --git a/test_data/gene_statistics/input/metadata1.csv b/test_data/gene_statistics/input/metadata1.csv
@@ -0,0 +1,5 @@
+ensembl_gene_id,name,description
+AT1G34790,TT1,C2H2 and C2HC zinc fingers superfamily protein
+AT5G35550,TT2,Duplicated homeodomain-like superfamily protein
+AT5G23260,TT16,K-box region and MADS-box transcription factor family protein
+AT5G23261,TT23,blabla
diff --git a/test_data/gene_statistics/input/metadata2.csv b/test_data/gene_statistics/input/metadata2.csv
@@ -0,0 +1,4 @@
+ensembl_gene_id,name,description
+AT1G34790,TT1,C2H2 and C2HC zinc fingers superfamily protein
+AT5G35550,TT2,Duplicated homeodomain-like superfamily protein
+AT5G23260,TT16,K-box region and MADS-box transcription factor family protein
diff --git a/test_data/idmapping/base/counts.ensembl_ids.csv b/test_data/idmapping/base/counts.ensembl_ids.csv
@@ -0,0 +1,4 @@
+ERR029909,ERR029910,ERR029911,ERR029912,ERR029913,ERR029914,ERR029915,ERR029916,ERR029917,ERR029918,ERR029920,ERR029921,ERR029922,ERR029923,ERR029924
+ENSRNA049434199,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+ENSRNA049434246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+ENSRNA049434252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
diff --git a/test_data/idmapping/base/counts.ncbi_ids.csv b/test_data/idmapping/base/counts.ncbi_ids.csv
@@ -0,0 +1,4 @@
+ERR029909,ERR029910,ERR029911,ERR029912,ERR029913,ERR029914,ERR029915,ERR029916,ERR029917,ERR029918,ERR029920,ERR029921,ERR029922,ERR029923,ERR029924
+840386,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+833520,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+832390,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
diff --git a/test_data/idmapping/base/counts.uniprot_ids.csv b/test_data/idmapping/base/counts.uniprot_ids.csv
@@ -0,0 +1,4 @@
+ERR029909,ERR029910,ERR029911,ERR029912,ERR029913,ERR029914,ERR029915,ERR029916,ERR029917,ERR029918,ERR029920,ERR029921,ERR029922,ERR029923,ERR029924
+Q8VWG3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+Q9FJA2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+Q8RYD9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
diff --git a/test_data/idmapping/custom/mapping.csv b/test_data/idmapping/custom/mapping.csv
@@ -0,0 +1,4 @@
+original_gene_id,ensembl_gene_id
+ENSRNA049434199,SNSRNA049434199
+ENSRNA049434246,SNSRNA049434246
+ENSRNA049434252,SNSRNA049434252
diff --git a/test_data/idmapping/empty/counts.csv b/test_data/idmapping/empty/counts.csv
@@ -0,0 +1 @@
+sample_1,sample_2,sample_3
diff --git a/test_data/idmapping/not_found/counts.csv b/test_data/idmapping/not_found/counts.csv
@@ -0,0 +1,4 @@
+sample_1,sample_2,sample_3
+8173941,1,2,3
+8168737,1,2,3
+8067017,1,2,3
diff --git a/test_data/input_datasets/input.csv b/test_data/input_datasets/input.csv
@@ -0,0 +1,3 @@
+counts,design,platform,normalised
+tests/test_data/custom_datasets/microarray.normalised.csv,tests/test_data/custom_datasets/microarray.normalised.design.csv,microarray,true
+tests/test_data/custom_datasets/rnaseq.raw.csv,tests/test_data/custom_datasets/rnaseq.raw.design.csv,rnaseq,false
diff --git a/test_data/input_datasets/microarray.normalised.csv b/test_data/input_datasets/microarray.normalised.csv
@@ -0,0 +1,10 @@
+,GSM1528575,GSM1528576,GSM1528579,GSM1528583,GSM1528584,GSM1528585,GSM1528580,GSM1528586,GSM1528582,GSM1528578,GSM1528581,GSM1528577
+ENSRNA049453121,20925.1255070264,136184.261516502,144325.370645564,89427.0987612997,164143.182734208,34178.6378088171,28842.7323281157,76973.395782103,41906.9367255656,44756.5602263121,252562.049703724,6953.65643340122
+ENSRNA049453138,196173.051628372,16607.8367703051,344972.83715281,22602.4535330758,13678.598561184,104546.421532852,15451.4637472048,71664.8857281649,160643.257448002,91459.0578537683,88396.7173963033,281623.08555275
+ENSRNA049454388,91547.4240932405,11625.4857392136,84483.143792525,80582.6604222701,218857.576978944,58304.7350856292,42234.0009090266,88475.1675656357,87306.1181782617,17513.436610296,90922.3378933406,76490.2207674135
+ENSRNA049454416,20925.1255070264,106290.155329953,193607.204524536,47170.3378081581,392119.825420608,190998.270108096,90648.5873169351,81397.1541603848,83813.8734511313,165404.67909724,111127.301869638,194702.380135234
+ENSRNA049454647,99394.3461583754,91343.1022366783,3520.13099135521,71738.2220832404,118547.854196928,20105.0810640101,81377.7090686122,15040.7784861581,66352.6498154789,110918.431865208,55563.6509348192,111258.50293442
+ENSRNA049454661,175247.926121346,66431.3470812206,24640.9169394865,52083.9146631746,360203.095444512,36189.1459152181,70046.6356539953,85820.9125386666,13968.9789085219,50594.3724297441,25256.2049703724,52152.4232505092
+ENSRNA049454747,117703.830977024,154452.881963838,281610.479308417,29481.4611300988,191500.379856576,152798.616086476,53565.0743236435,14156.0268105017,293348.557078959,155674.99209152,63140.5124259309,243377.975169043
+ENSRNA049454887,2615.6406883783,164417.584026021,28161.0479308417,82548.0911642767,50154.861391008,136714.551235268,97859.270398964,64586.872322914,328271.004350264,159566.866893808,151537.229822234,86920.7054175153
+ENSRNA049454931,177863.566809724,81378.4001744952,235848.776420799,88444.3833902964,18238.131414912,120630.48638406,82407.8066517592,50430.8455124123,118736.320722436,68107.8090400402,232357.085727426,163410.926184929
diff --git a/test_data/input_datasets/microarray.normalised.design.csv b/test_data/input_datasets/microarray.normalised.design.csv
@@ -0,0 +1,13 @@
+sample,condition
+GSM1528575,g1
+GSM1528576,g1
+GSM1528579,g1
+GSM1528583,g2
+GSM1528584,g2
+GSM1528585,g2
+GSM1528580,g3
+GSM1528586,g3
+GSM1528582,g3
+GSM1528578,g4
+GSM1528581,g4
+GSM1528577,g4
diff --git a/test_data/input_datasets/rnaseq.raw.csv b/test_data/input_datasets/rnaseq.raw.csv
@@ -0,0 +1,10 @@
+,ESM1528575,ESM1528576,ESM1528579,ESM1528583,ESM1528584,ESM1528585,ESM1528580,ESM1528586,ESM1528582,ESM1528578,ESM1528581,ESM1528577
+ENSRNA049453121,1,82,8,82,4,68,88,73,46,57,25,22
+ENSRNA049453138,68,93,41,84,36,18,28,92,84,85,92,32
+ENSRNA049454388,38,10,0,23,11,17,95,57,25,82,10,70
+ENSRNA049454416,75,55,7,30,79,60,15,97,12,35,60,56
+ENSRNA049454647,35,64,55,91,48,95,68,100,24,26,100,47
+ENSRNA049454661,8,99,80,48,86,29,80,17,19,9,44,2
+ENSRNA049454747,67,7,98,53,3,10,52,87,4,80,22,15
+ENSRNA049454887,8,40,24,90,42,52,79,81,94,23,35,81
+ENSRNA049454931,45,49,67,73,26,76,41,16,34,47,36,25
diff --git a/test_data/input_datasets/rnaseq.raw.design.csv b/test_data/input_datasets/rnaseq.raw.design.csv
@@ -0,0 +1,13 @@
+sample,condition
+ESM1528575,g1
+ESM1528576,g1
+ESM1528579,g1
+ESM1528583,g2
+ESM1528584,g2
+ESM1528585,g2
+ESM1528580,g3
+ESM1528586,g3
+ESM1528582,g3
+ESM1528578,g4
+ESM1528581,g4
+ESM1528577,g4
diff --git a/test_data/merge_data/input/counts1.parquet b/test_data/merge_data/input/counts1.parquet
diff --git a/test_data/merge_data/input/counts2.parquet b/test_data/merge_data/input/counts2.parquet
diff --git a/test_data/merge_data/input/counts3.parquet b/test_data/merge_data/input/counts3.parquet
diff --git a/test_data/merge_data/input/dataset_stat1.csv b/test_data/merge_data/input/dataset_stat1.csv
@@ -0,0 +1,10 @@
+sample,count,skewness,kolmogorov_smirnov_to_uniform_dist_pvalue
+ARR029909,1,1,1
+ARR029910,2,3,1
+ARR029911,3,5,1
+ARR029912,4,4,9
+ARR029913,5,1,5
+ARR029914,6,6,6
+ARR029915,7,1,9
+ARR029916,8,8,1
+ARR029917,9,3,9
diff --git a/test_data/merge_data/input/dataset_stat2.csv b/test_data/merge_data/input/dataset_stat2.csv
@@ -0,0 +1,10 @@
+sample,count,skewness,kolmogorov_smirnov_to_uniform_dist_pvalue
+URR029909,1,1,1
+URR029910,2,2,2
+URR029911,3,2,3
+URR029912,4,4,4
+URR029913,5,5,5
+URR029914,6,6,3
+URR029915,7,7,7
+URR029916,8,8,8
+URR029917,9,9,9
diff --git a/test_data/merge_data/input/dataset_stat3.csv b/test_data/merge_data/input/dataset_stat3.csv
@@ -0,0 +1,10 @@
+sample,count,skewness,kolmogorov_smirnov_to_uniform_dist_pvalue
+ERR029909,1,1,1
+ERR029910,2,2,2
+ERR029911,3,3,3
+ERR029912,4,9,4
+ERR029913,5,5,5
+ERR029914,6,6,6
+ERR029915,7,7,7
+ERR029916,8,8,1
+ERR029917,9,9,9
diff --git a/test_data/merge_data/input/design1.csv b/test_data/merge_data/input/design1.csv
@@ -0,0 +1,10 @@
+sample,condition
+ARR029909,g1
+ARR029910,g1
+ARR029911,g1
+ARR029912,g2
+ARR029913,g2
+ARR029914,g2
+ARR029915,g3
+ARR029916,g3
+ARR029917,g3
diff --git a/test_data/merge_data/input/design2.csv b/test_data/merge_data/input/design2.csv
@@ -0,0 +1,10 @@
+sample,condition
+URR029909,g1
+URR029910,g1
+URR029911,g1
+URR029912,g2
+URR029913,g2
+URR029914,g2
+URR029915,g3
+URR029916,g3
+URR029917,g3
diff --git a/test_data/merge_data/input/design3.csv b/test_data/merge_data/input/design3.csv
@@ -0,0 +1,10 @@
+batch,sample,condition
+batch3,ERR029909,g1
+batch3,ERR029910,g1
+batch3,ERR029911,g1
+batch3,ERR029912,g2
+batch3,ERR029913,g2
+batch3,ERR029914,g2
+batch3,ERR029915,g3
+batch3,ERR029916,g3
+batch3,ERR029917,g3
diff --git a/test_data/merge_data/output/all_counts.csv b/test_data/merge_data/output/all_counts.csv
@@ -0,0 +1,15 @@
+ensembl_gene_id,URR029909,URR029910,URR029911,URR029912,URR029913,URR029914,URR029915,URR029916,URR029917,ERR029909,ERR029910,ERR029911,ERR029912,ERR029913,ERR029914,ERR029915,ERR029916,ERR029917,ARR029909,ARR029910,ARR029911,ARR029912,ARR029913,ARR029914,ARR029915,ARR029916,ARR029917
+AT1G34790,0.60113057,0.64080682,0.6,0.6197164000000003,0.60115891,0.63052843,0.61002869,0.65849011,0.66239896,0.60113057,0.64080682,0.6348181099999999,0.6519716400000001,0.60115891,0.63052843,0.61002869,0.65849011,0.66239896,0.60113057,0.64080682,0.6348181099999999,0.6519716400000001,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896
+AT5G35550,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.0,0.8336608,0.00340416,0.23179154000000002,0.0,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002
+AT5G23260,0.71122807,0.47981484,0.85599454,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134,0.71122807,0.47981484,0.85599454,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134,0.71122807,0.47981484,0.85599454,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134
+AT1G34791,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896
+AT5G35551,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.0,0.00340416,0.23179154000000002,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002
+AT5G23261,0.71122807,0.47981484,0.85599454,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134,0.71122807,0.47981484,0.85599454,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134,0.71122807,0.47981484,0.85599454,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134
+AT1G34792,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.0,0.93052843,0.71002869,0.65849011,0.16239896,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896
+AT5G35552,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002,0.7148504699999999,0.21713193,0.03318757,0.18404821999999998,0.70246917,0.7555268599999999,0.8336608,0.00340416,0.23179154000000002
+AT5G23262,0.0,0.47981484,0.85599454,0.69023553,0.0,0.30220852000000004,0.73996866,0.08559519,0.80013134,0.71122807,0.47981484,0.85599454,0.0,0.0,0.0,0.73996866,0.0,0.0,0.0,0.0,0.0,0.69023553,0.40420572,0.30220852000000004,0.73996866,0.08559519,0.80013134
+AT1G34793,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.0,0.93052843,0.71002869,0.65849011,0.16239896,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896,0.60113057,0.64080682,0.9348181099999999,0.35197164000000003,0.20115891000000002,0.93052843,0.71002869,0.65849011,0.16239896
+AT5G35553,,0.21713193,,,,,,,,,,,,,0,,,,,0.9348181099999999,,,0.35197164000000003,,,,0.0
+AT5G35554,,0.01713193,,,,,,,,,,,,,0.01,,,,,0.15,,,0.151,,,,0.0114
+AT5G35555,,0.01713193,,,,,0.0,,,,,,,,0.01,,,,,0.0,,,0.151,,,,0.011
+AT5G23263,,,,,,,,,,,,,,,,,,,,,,,,,,,
diff --git a/test_data/merge_data/output/all_counts.parquet b/test_data/merge_data/output/all_counts.parquet
diff --git a/test_data/normalisation/base/counts.csv b/test_data/normalisation/base/counts.csv
@@ -0,0 +1,13 @@
+,E_MTAB_5038_rnaseq_SRR1586392,E_MTAB_5038_rnaseq_SRR1586393,E_MTAB_5038_rnaseq_SRR1586394,E_MTAB_5038_rnaseq_SRR1586395,E_MTAB_5038_rnaseq_SRR1586396,E_MTAB_5038_rnaseq_SRR1586397,E_MTAB_5038_rnaseq_SRR1586400,E_MTAB_5038_rnaseq_SRR1586401,E_MTAB_5038_rnaseq_SRR1586402
+ENSRNA549434199,14,25,27,47,39,34,38,19,64
+ENSRNA549434200,91,37,78,84,6,51,18,2,57
+ENSRNA549434201,98,48,69,7,73,48,57,92,36
+ENSRNA549434202,52,15,41,19,8,100,85,83,97
+ENSRNA549434203,86,71,53,16,66,23,12,42,33
+ENSRNA549434204,62,2,25,89,74,32,45,56,26
+ENSRNA549434205,98,42,79,76,74,85,3,91,56
+ENSRNA549434206,42,49,4,88,82,34,27,83,98
+ENSRNA549434207,82,93,85,14,38,8,98,97,30
+ENSRNA549434208,72,36,4,60,25,7,14,76,47
+ENSRNA549434209,65,12,99,82,72,52,24,79,31
+ENSRNA549434210,0,0,0,0,0,0,0,0,0
diff --git a/test_data/normalisation/base/design.csv b/test_data/normalisation/base/design.csv
@@ -0,0 +1,10 @@
+batch,condition,sample
+E_MTAB_5038_rnaseq,g1,E_MTAB_5038_rnaseq_SRR1586392
+E_MTAB_5038_rnaseq,g1,E_MTAB_5038_rnaseq_SRR1586393
+E_MTAB_5038_rnaseq,g1,E_MTAB_5038_rnaseq_SRR1586394
+E_MTAB_5038_rnaseq,g2,E_MTAB_5038_rnaseq_SRR1586395
+E_MTAB_5038_rnaseq,g2,E_MTAB_5038_rnaseq_SRR1586396
+E_MTAB_5038_rnaseq,g2,E_MTAB_5038_rnaseq_SRR1586397
+E_MTAB_5038_rnaseq,g3,E_MTAB_5038_rnaseq_SRR1586400
+E_MTAB_5038_rnaseq,g3,E_MTAB_5038_rnaseq_SRR1586401
+E_MTAB_5038_rnaseq,g3,E_MTAB_5038_rnaseq_SRR1586402
diff --git a/test_data/normalisation/many_zeros/counts.csv b/test_data/normalisation/many_zeros/counts.csv
@@ -0,0 +1,6 @@
+,E_CURD_1_rnaseq_ERR274309,E_CURD_1_rnaseq_ERR274310,E_CURD_1_rnaseq_SRR070570,E_CURD_1_rnaseq_SRR070571,E_CURD_1_rnaseq_SRR1001909,E_CURD_1_rnaseq_SRR1001910,E_CURD_1_rnaseq_SRR1019221,E_CURD_1_rnaseq_SRR1046909,E_CURD_1_rnaseq_SRR1046910,E_CURD_1_rnaseq_SRR1105822,E_CURD_1_rnaseq_SRR1105823,E_CURD_1_rnaseq_SRR1106559,E_CURD_1_rnaseq_SRR1159821,E_CURD_1_rnaseq_SRR1159827,E_CURD_1_rnaseq_SRR1159831,E_CURD_1_rnaseq_SRR1159837,E_CURD_1_rnaseq_SRR949993
+AT1G80990,0,0,1,0,1,1,0,0,1,1,3,0,0,1,1,1,0
+AT2G01008,11,24,3,4,6,4,0,0,2,0,0,1,4,2,4,4,0
+AT2G01010,9,1,195,195,8,33,0,14,7,0,0,2,1,0,0,0,0
+AT2G01020,34,27,41,55,58,107,2,10,20,1,3,1,4,2,3,0,0
+AT2G01021,22,10,0,0,0,0,0,106,20,0,0,1,0,0,0,0,0
diff --git a/test_data/normalisation/many_zeros/design.csv b/test_data/normalisation/many_zeros/design.csv
@@ -0,0 +1,18 @@
+batch,condition,sample
+E_CURD_1_rnaseq,g2,E_CURD_1_rnaseq_ERR274309
+E_CURD_1_rnaseq,g3,E_CURD_1_rnaseq_ERR274310
+E_CURD_1_rnaseq,g23,E_CURD_1_rnaseq_SRR070570
+E_CURD_1_rnaseq,g23,E_CURD_1_rnaseq_SRR070571
+E_CURD_1_rnaseq,g55,E_CURD_1_rnaseq_SRR1001909
+E_CURD_1_rnaseq,g55,E_CURD_1_rnaseq_SRR1001910
+E_CURD_1_rnaseq,g56,E_CURD_1_rnaseq_SRR1019221
+E_CURD_1_rnaseq,g48,E_CURD_1_rnaseq_SRR1046909
+E_CURD_1_rnaseq,g48,E_CURD_1_rnaseq_SRR1046910
+E_CURD_1_rnaseq,g50,E_CURD_1_rnaseq_SRR1105822
+E_CURD_1_rnaseq,g50,E_CURD_1_rnaseq_SRR1105823
+E_CURD_1_rnaseq,g50,E_CURD_1_rnaseq_SRR1106559
+E_CURD_1_rnaseq,g6,E_CURD_1_rnaseq_SRR1159821
+E_CURD_1_rnaseq,g6,E_CURD_1_rnaseq_SRR1159827
+E_CURD_1_rnaseq,g6,E_CURD_1_rnaseq_SRR1159831
+E_CURD_1_rnaseq,g6,E_CURD_1_rnaseq_SRR1159837
+E_CURD_1_rnaseq,g44,E_CURD_1_rnaseq_SRR949993
diff --git a/test_data/normalisation/one_group/counts.csv b/test_data/normalisation/one_group/counts.csv
@@ -0,0 +1,6 @@
+sampleA,sampleB,sampleC,sampleD
+ENSG00000000003,14,4,4,10
+ENSG00000000005,0,0,0,0
+ENSG00000000419,562,584,523,616
+ENSG00000000457,586,377,207,491
+ENSG00000000460,130,55,28,77
diff --git a/test_data/normalisation/one_group/design.csv b/test_data/normalisation/one_group/design.csv
@@ -0,0 +1,5 @@
+batch,condition,sample
+batch1,g1,sampleA
+batch1,g1,sampleB
+batch1,g1,sampleC
+batch1,g1,sampleD
diff --git a/test_data/quantile_normalisation/count.raw.cpm.csv b/test_data/quantile_normalisation/count.raw.cpm.csv
@@ -0,0 +1,10 @@
+,sample_63,sample_64,sample_65,sample_66,sample_67,sample_68,sample_69,sample_70
+ENSRNA049454747,9.07095165125094,56.5509090498679,12.6897789869867,15.7656784862991,4.55005160208214,5.21967362537592,8.87627280506172,6.33326316409849
+ENSRNA049454887,0.740485849081709,1.66326203087847,0.229679257683017,0.785665040845472,2.20608562525195,2.37257892062542,0.365278716257684,0.139192597013154
+ENSRNA049454931,1.20328950475778,2.61369747709473,0.574198144207542,1.46657474291155,2.0682052736737,3.32161048887559,0.620973817638062,0.591568537305903
+ENSRNA049454947,1.48097169816342,2.1384797539866,0.459358515366033,1.57133008169094,2.89548738314318,3.08435259681304,0.474862331134989,0.452375940292749
+ENSRNA049454955,1.29585023589299,2.61369747709473,0.516778329786788,1.09993105718366,3.8606498441909,4.03338416506321,0.584445946012294,0.452375940292749
+ENSRNA049454963,1.38841096702821,4.51456836952727,1.43549536051885,2.7236388082643,4.96369265681688,5.45693151743846,1.35153125015343,1.25273337311838
+ENSRNA049454974,1.66609316043385,3.564132923311,2.52647183451318,2.46175046131581,5.51521406312986,12.5746682793147,1.71680996641111,1.53111856714469
+ENSRNA049455639,0.185121462270427,0.237608861554067,0.803877401890558,1.15230872657336,0.137880351578247,0.237257892062542,0.438334459509221,0.417577791039461
+ENSRNA049455690,0.0925607311352137,1.18804430777033,0.746457587469804,2.98552715521279,0.137880351578247,0.237257892062542,0.876668919018441,0.487174089546038