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refactor: update the HTML report (#30)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| <!DOCTYPE html> | ||
| <html> | ||
| <head> | ||
| <title>MAPP reports</title> | ||
| </head> | ||
| <body style="background-color: rgb(219, 219, 219)"> | ||
| <br> | ||
| <center> | ||
| <img src=mapp_logo.png width="4%"> | ||
| <h1>MAPP Report</h1> | ||
| <h3>Test run with reduced parameters on a sampled dataset</h3> | ||
| <br> | ||
| <a href="gene-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Gene Expression</button> | ||
| </a> | ||
| | ||
| <a href="transcript-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Transcript Expression</button> | ||
| </a> | ||
| | ||
| <a href="exon-inclusion.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Exon Inclusion Fractions</button> | ||
| </a> | ||
| | ||
| <a href="pas-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Poly(A) Site Expressions</button> | ||
| </a> | ||
| <br> | ||
| <br> | ||
| <a href="activities-3ss.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid #33a02c; background-color: #ffffff">3'SS Activities & Counts</button> | ||
| </a> | ||
| | ||
| <a href="activities-5ss.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">5'SS Activities & Counts</button> | ||
| </a> | ||
| | ||
| <a href="activities-pas.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">PAS Activities & Counts</button> | ||
| </a> | ||
| </center> | ||
| <br> | ||
| <br> | ||
| <center> | ||
| <div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;"> | ||
| This is a summary report for a MAPP run. | ||
| Motif count matrices are located under: <code>../modules/CREATE_SITECOUNT_MATRICES/output</code>, | ||
| unless external pre-computer resources were specified for this specific workflow execution. | ||
| In such case please refer to the pipeline's configuration file and inspect the paths provided | ||
| under the field: <code>MAE_sitecount_matrices</code>. | ||
| <br> | ||
| <br> | ||
| Fitted motif activities as well as calculated activity z-scores and their statistical significance | ||
| are stored in a tab-separated formatted (TSV) table. | ||
| Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the | ||
| structure below: | ||
| <br> | ||
| <br> | ||
| <b>ID</b> : unique ID of a sequence motif in a specific sliding window | ||
| <br> | ||
| <b>activities_{sampleID}</b> : motif activities in distinct RNA-Seq samples | ||
| <br> | ||
| <b>deltas_{sampleID}</b> : standard deviations of motif activities | ||
| <br> | ||
| <b>zscores_{sampleID}</b> : z-scores of motif activities | ||
| <br> | ||
| <b>combined.Zscore</b> : overall z-score for a given motif, combined over all samples | ||
| <br> | ||
| <b>regions_present_fraction</b> : fraction of sites for which the motif was present in a specific window | ||
| <br> | ||
| <b>region</b> : sliding window ID | ||
| <br> | ||
| <b>motif</b> : short sequence motif | ||
| <br> | ||
| <b>standard_zscores_{sampleID}</b> : standardised z-scores of motif activities | ||
| <br> | ||
| <b>pval_{sampleID}</b> : standardised p-values of motif activities | ||
| <br> | ||
| <b>corr_pval_{sampleID}</b> : p-values corrected for multiple hypothesis testing | ||
| <br> | ||
| <b>combined.standard.Zscore</b> : combined standardised z-scores | ||
| <br> | ||
| <b>max.abs.standard.Zscore</b> : maximum absolute standardised z-score | ||
| <br> | ||
| <b>significance-marker</b> : statistical significance marker for this motif in this sliding window | ||
| <br> | ||
| <br> | ||
| </div> | ||
| <br> | ||
| <a href="report.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Main Menu</button> | ||
| </a> | ||
| | ||
| <a href="results/results-3ss.tsv" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Download Table</button> | ||
| </a> | ||
| </center> | ||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| <!DOCTYPE html> | ||
| <html> | ||
| <head> | ||
| <title>MAPP reports</title> | ||
| </head> | ||
| <body style="background-color: rgb(219, 219, 219)"> | ||
| <br> | ||
| <center> | ||
| <img src=mapp_logo.png width="4%"> | ||
| <h1>MAPP Report</h1> | ||
| <h3>Test run with reduced parameters on a sampled dataset</h3> | ||
| <br> | ||
| <a href="gene-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Gene Expression</button> | ||
| </a> | ||
| | ||
| <a href="transcript-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Transcript Expression</button> | ||
| </a> | ||
| | ||
| <a href="exon-inclusion.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Exon Inclusion Fractions</button> | ||
| </a> | ||
| | ||
| <a href="pas-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Poly(A) Site Expressions</button> | ||
| </a> | ||
| <br> | ||
| <br> | ||
| <a href="activities-3ss.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">3'SS Activities & Counts</button> | ||
| </a> | ||
| | ||
| <a href="activities-5ss.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid #33a02c; background-color: #ffffff">5'SS Activities & Counts</button> | ||
| </a> | ||
| | ||
| <a href="activities-pas.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">PAS Activities & Counts</button> | ||
| </a> | ||
| </center> | ||
| <br> | ||
| <br> | ||
| <center> | ||
| <div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;"> | ||
| This is a summary report for a MAPP run. | ||
| Motif count matrices are located under: <code>../modules/CREATE_SITECOUNT_MATRICES/output</code>, | ||
| unless external pre-computer resources were specified for this specific workflow execution. | ||
| In such case please refer to the pipeline's configuration file and inspect the paths provided | ||
| under the field: <code>MAE_sitecount_matrices</code>. | ||
| <br> | ||
| <br> | ||
| Fitted motif activities as well as calculated activity z-scores and their statistical significance | ||
| are stored in a tab-separated formatted (TSV) table. | ||
| Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the | ||
| structure below: | ||
| <br> | ||
| <br> | ||
| <b>ID</b> : unique ID of a sequence motif in a specific sliding window | ||
| <br> | ||
| <b>activities_{sampleID}</b> : motif activities in distinct RNA-Seq samples | ||
| <br> | ||
| <b>deltas_{sampleID}</b> : standard deviations of motif activities | ||
| <br> | ||
| <b>zscores_{sampleID}</b> : z-scores of motif activities | ||
| <br> | ||
| <b>combined.Zscore</b> : overall z-score for a given motif, combined over all samples | ||
| <br> | ||
| <b>regions_present_fraction</b> : fraction of sites for which the motif was present in a specific window | ||
| <br> | ||
| <b>region</b> : sliding window ID | ||
| <br> | ||
| <b>motif</b> : short sequence motif | ||
| <br> | ||
| <b>standard_zscores_{sampleID}</b> : standardised z-scores of motif activities | ||
| <br> | ||
| <b>pval_{sampleID}</b> : standardised p-values of motif activities | ||
| <br> | ||
| <b>corr_pval_{sampleID}</b> : p-values corrected for multiple hypothesis testing | ||
| <br> | ||
| <b>combined.standard.Zscore</b> : combined standardised z-scores | ||
| <br> | ||
| <b>max.abs.standard.Zscore</b> : maximum absolute standardised z-score | ||
| <br> | ||
| <b>significance-marker</b> : statistical significance marker for this motif in this sliding window | ||
| <br> | ||
| <br> | ||
| </div> | ||
| <br> | ||
| <a href="report.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Main Menu</button> | ||
| </a> | ||
| | ||
| <a href="results/results-5ss.tsv" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Download Table</button> | ||
| </a> | ||
| </center> | ||
| </body> | ||
| </html> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| <!DOCTYPE html> | ||
| <html> | ||
| <head> | ||
| <title>MAPP reports</title> | ||
| </head> | ||
| <body style="background-color: rgb(219, 219, 219)"> | ||
| <br> | ||
| <center> | ||
| <img src=mapp_logo.png width="4%"> | ||
| <h1>MAPP Report</h1> | ||
| <h3>Test run with reduced parameters on a sampled dataset</h3> | ||
| <br> | ||
| <a href="gene-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Gene Expression</button> | ||
| </a> | ||
| | ||
| <a href="transcript-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Transcript Expression</button> | ||
| </a> | ||
| | ||
| <a href="exon-inclusion.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Exon Inclusion Fractions</button> | ||
| </a> | ||
| | ||
| <a href="pas-expression.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Poly(A) Site Expressions</button> | ||
| </a> | ||
| <br> | ||
| <br> | ||
| <a href="activities-3ss.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">3'SS Activities & Counts</button> | ||
| </a> | ||
| | ||
| <a href="activities-5ss.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">5'SS Activities & Counts</button> | ||
| </a> | ||
| | ||
| <a href="activities-pas.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid #33a02c; background-color: #ffffff">PAS Activities & Counts</button> | ||
| </a> | ||
| </center> | ||
| <br> | ||
| <br> | ||
| <center> | ||
| <div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;"> | ||
| This is a summary report for a MAPP run. | ||
| Motif count matrices are located under: <code>../modules/KAPAC/output</code>, | ||
| unless external pre-computer resources were specified for this specific workflow execution. | ||
| In such case please refer to the pipeline's configuration file and inspect the paths provided | ||
| under the field: <code>KPC_sitecount_matrices</code>. | ||
| <br> | ||
| <br> | ||
| Fitted motif activities as well as calculated activity z-scores and their statistical significance | ||
| are stored in a tab-separated formatted (TSV) table. | ||
| Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the | ||
| structure below: | ||
| <br> | ||
| <br> | ||
| <b>ID</b> : unique ID of a sequence motif in a specific sliding window | ||
| <br> | ||
| <b>activities_{sampleID}</b> : motif activities in distinct RNA-Seq samples | ||
| <br> | ||
| <b>deltas_{sampleID}</b> : standard deviations of motif activities | ||
| <br> | ||
| <b>zscores_{sampleID}</b> : z-scores of motif activities | ||
| <br> | ||
| <b>combined.Zscore</b> : overall z-score for a given motif, combined over all samples | ||
| <br> | ||
| <b>regions_present_fraction</b> : fraction of sites for which the motif was present in a specific window | ||
| <br> | ||
| <b>region</b> : sliding window ID | ||
| <br> | ||
| <b>motif</b> : short sequence motif | ||
| <br> | ||
| <b>standard_zscores_{sampleID}</b> : standardised z-scores of motif activities | ||
| <br> | ||
| <b>pval_{sampleID}</b> : standardised p-values of motif activities | ||
| <br> | ||
| <b>corr_pval_{sampleID}</b> : p-values corrected for multiple hypothesis testing | ||
| <br> | ||
| <b>combined.standard.Zscore</b> : combined standardised z-scores | ||
| <br> | ||
| <b>max.abs.standard.Zscore</b> : maximum absolute standardised z-score | ||
| <br> | ||
| <b>significance-marker</b> : statistical significance marker for this motif in this sliding window | ||
| <br> | ||
| <br> | ||
| </div> | ||
| <br> | ||
| <a href="report.html" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Main Menu</button> | ||
| </a> | ||
| | ||
| <a href="results/results-pas.tsv" style="text-decoration: none;"> | ||
| <button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Download Table</button> | ||
| </a> | ||
| </center> | ||
| </body> | ||
| </html> |
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