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markziemann committed Feb 7, 2019
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6 changes: 3 additions & 3 deletions frontend/html/about.html
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Expand Up @@ -191,16 +191,16 @@ <h2 id="content">Latest News</h2>
</p>
<ul style="list-style-type:circle">
<li>&bull;Data bundles: any project with >200 runs we've collected into bundles which can be downloaded <a href="/bundles">here</a>. </li><br><br>
<li>&bull;Keyword searches: users can now string together multiple keywords with "and" to restrict the search results. Multiple word search terms also wrk better now.</li><br><br>
<li>&bull;Keyword searches: users can now string together multiple keywords with "and" to restrict the search results. Multiple word search terms also work now.</li><br><br>
<li>&bull;Metadata: Now when you perform a search with the web UI, the experiment.name from SRA is shown and hopefully this will make it easier to perform downstream analysis. Also
we have included full and summary metadata in each DEE2 download. The metadata are also available for download from the bulk page.</li><br><br>
<li>&bull;R API: previously the API code was sourced from GitHub, due to some security concerns we now have a package on github which can be installed with devtools.</li><br><br>
<li>&bull;You will also notice two new files in each download GeneInfo.tsv and TxInfo.tsv. These contain the gene symbols information as well as the gene and transcript lengths for FPKM calculation.
Importantly, the TxInfo.tsv contains the tx-->parent gene information so that transcript data can be easily aggregated to the gene level. In the R package, there is a new function called Tx2Gene
which performs aggregation (sum) with a single command "x<-Tx2Gene(x)". </li><br><br>
<li>&bull;QC classification: We have just implemented QC thresholds to classify datasets as pass, warn or fail. More infor on this can be found
<li>&bull;QC classification: We have just implemented QC thresholds to classify datasets as pass, warn or fail. More information on this can be found
<a href="https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md" >here</a></li><br><br>
<li>&bull;Kallisto TPM: In addition to being able to caluculate FPKM using the R API, you can get Kallisto TPM from the repository for individual runs. Here is an example:
<li>&bull;Kallisto TPM: In addition to being able to calculate FPKM using the R API, you can get Kallisto TPM from the repository for individual runs. Here is an example:
<a href="http://dee2.io/data/dmelanogaster/SRR1991949" target="_blank">SRR1991949</a>. The kallisto output file has the "ke.tsv.gz" suffix.</li><br><br>
</ul>

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7 changes: 0 additions & 7 deletions frontend/html/index.html
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Expand Up @@ -157,13 +157,6 @@ <h1>Digital Expression Explorer 2
<p>Digital Expression Explorer 2 (DEE2) is a repository of uniformly processed RNA-seq data mined from public data obtained from <a href="http://www.ncbi.nlm.nih.gov/sra" target="_blank"> NCBI Short
Read Archive.</a></p>

<h2>Users please note
</h2>

<p> Data processing is still underway and these pages are still under construction until the official announcement day.
Any feedback is appreciated.
</p>

<h2>Hosted RNA-seq data
</h2>

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