Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_data.xml @ 16:0ce8b8d2322f draft

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"planemo upload commit 889d13f87b8ee67aabc4a773cd55cea7285fe08b-dirty"
author proteore
date Fri, 24 Jan 2020 08:25:34 +0000
parents 64681d9836e7
children 5d21c5e70774
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15:64681d9836e7 16:0ce8b8d2322f
1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.23.3"> 1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.2'">
2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas] 2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.4">R</requirement> 5 <requirement type="package" version="3.4.4">R</requirement>
6 </requirements> 6 </requirements>
135 135
136 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa 136 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa
137 137
138 - RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. 138 - RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts.
139 139
140 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. 140 - RNA non-specific tissue abundance in 'Transcript Per Million' (only available from 23/10/2018 release): please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
141 141
142 ----- 142 -----
143 143
144 **Output** 144 **Output**
145 145
146 The output is a tabular file containing initial columns and new columns with annotation from HPA. 146 The output is a tabular file containing initial columns and new columns with annotation from HPA.
147 147
148 ----- 148 -----
149 149
150 **Data sources (release date)** 150 **HPA source file version (release date)**
151 151
152 HPA source file (data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38): http://www.proteinatlas.org/download/proteinatlas.tab.gz 152 Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38
153
154 Release date 21/01/2020: a subset of the data in the Human Protein Atlas version 19.1
155
156 downloaded from: http://www.proteinatlas.org/download/proteinatlas.tab.gz
153 157
154 ----- 158 -----
155 159
156 .. class:: infomark 160 .. class:: infomark
157 161