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‎_sources/ggd-search.rst.txt‎

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@@ -723,7 +723,7 @@ Some examples of using the `ggd search` tool:
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5. Example of searching for two different data packages at the same time for a specific genome build
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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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The default behavior is to serach for terms both combine and seperatly. Therefore, one does noes need
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The default behavior is to search for terms both combine and separately. Therefore, one does noes need
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to set the :code:`--search-type` unless they would like to refine the results. The example below can also
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be done with setting search-type flag as such: :code:`--search type non-combined-only`
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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In this example the :code:`--search-term` flag is set to `combined-only`. This is often done when you know which
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package you want but don't know the exact package name. This will refnie the results to those based on a combination
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package you want but don't know the exact package name. This will refine the results to those based on a combination
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of the terms provided.
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.. code-block:: bash

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-cds-only-features-ensembl-v1/README.rst.txt‎

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.. _`grch37-cds-only-features-ensembl-v1`:
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grch37-cds-only-features-ensembl-v1
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===================================
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|downloads|
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CDS only features from Ensembl gene sets. All other features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: CDS. Features are in GTF format.
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================================== ====================================
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GGD Package grch37-cds-only-features-ensembl-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider Ensembl
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Data Version release-75_2-6-14
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-cds-only-features-ensembl-v1.gtf.gz, grch37-cds-only-features-ensembl-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-cds-only-features-ensembl-v1.gtf.gz: **10.78M**, grch37-cds-only-features-ensembl-v1.gtf.gz.tbi: **501.40K**
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Package Keywords Gene-Features, GTF, Ensembl-GTF, Ensembl-Gene-Set, Annotated-Transcripts, CDS-Only-Features
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Package Dependencies: gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-cds-only-features-ensembl-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-cds-only-features-ensembl-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-cds-only-features-ensembl-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-cds-only-features-ensembl-v1

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-cds-only-features-gencode-v1/README.rst.txt‎

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.. _`grch37-cds-only-features-gencode-v1`:
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grch37-cds-only-features-gencode-v1
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===================================
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|downloads|
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CDS only features from the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All other features have been removed. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: CDS.
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================================== ====================================
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GGD Package grch37-cds-only-features-gencode-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider GENCODE
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Data Version release-34_03-24-2020
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-cds-only-features-gencode-v1.gtf.gz, grch37-cds-only-features-gencode-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-cds-only-features-gencode-v1.gtf.gz: **21.08M**, grch37-cds-only-features-gencode-v1.gtf.gz.tbi: **517.43K**
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Package Keywords Gene-Features, GTF, GENOCDOE-GTF, GENCODE-Gene-Sets, Annotated-Transcripts, CDS-Only-Features
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Package Dependencies: grch37-chrom-mapping-ucsc2ensembl-ncbi-v1, gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-cds-only-features-gencode-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-cds-only-features-gencode-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-cds-only-features-gencode-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-cds-only-features-gencode-v1

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-protein-coding-features-ensembl-v1/README.rst.txt‎

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.. _`grch37-protein-coding-features-ensembl-v1`:
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grch37-protein-coding-features-ensembl-v1
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=========================================
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|downloads|
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Protein Coding Features based on feature's gene biotype from Ensembl gene sets. All non-protein coding features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: CDS, Selenocysteine, UTR, exon, gene, start_codon, stop_codon, transcript. Features are in GTF format.
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================================== ====================================
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GGD Package grch37-protein-coding-features-ensembl-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider Ensembl
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Data Version release-75_2-6-14
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-protein-coding-features-ensembl-v1.gtf.gz, grch37-protein-coding-features-ensembl-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-protein-coding-features-ensembl-v1.gtf.gz: **35.31M**, grch37-protein-coding-features-ensembl-v1.gtf.gz.tbi: **228.59K**
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Package Keywords Gene-Features, GTF, Ensembl-GTF, Ensembl-Gene-Set, Annotated-Transcripts, Protein-Coding-Features
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Package Dependencies: gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-protein-coding-features-ensembl-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-protein-coding-features-ensembl-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-protein-coding-features-ensembl-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-protein-coding-features-ensembl-v1

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-protein-coding-features-gencode-v1/README.rst.txt‎

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.. _`grch37-protein-coding-features-gencode-v1`:
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grch37-protein-coding-features-gencode-v1
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=========================================
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|downloads|
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Protein Coding Features based on feature's gene biotype from the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All non-protein coding features have been removed. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: CDS, Selenocysteine, UTR, exon, gene, start_codon, stop_codon, transcript.
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================================== ====================================
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GGD Package grch37-protein-coding-features-gencode-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider GENCODE
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Data Version release-34_03-24-2020
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-protein-coding-features-gencode-v1.gtf.gz, grch37-protein-coding-features-gencode-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-protein-coding-features-gencode-v1.gtf.gz: **60.21M**, grch37-protein-coding-features-gencode-v1.gtf.gz.tbi: **244.29K**
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Package Keywords Gene-Features, GTF, GENOCDOE-GTF, GENCODE-Gene-Sets, Annotated-Transcripts, Protein-Coding-Features
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Package Dependencies: grch37-chrom-mapping-ucsc2ensembl-ncbi-v1, gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-protein-coding-features-gencode-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-protein-coding-features-gencode-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-protein-coding-features-gencode-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-protein-coding-features-gencode-v1

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-scores-by-amino-acid-change-ggd-v1/README.rst.txt‎

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|downloads|
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missense badnass, blosum, grantham scores foreach amino acid change
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Scores for each amino acid changes from missense badnass, blosum, and granthams
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================================== ====================================
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GGD Package grch37-scores-by-amino-acid-change-ggd-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author bsp
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Recipe Author mjc
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Data Provider ggd
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Data Version 1
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Genomic File Type txt
2020
Data file coordinate basing NA
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Package's Data Files grch37-scores-by-amino-acid-change-ggd-v1.txt
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Approximate Size of Each Data File NA
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Package Keywords amino-acid, constraint
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Approximate Size of Each Data File grch37-scores-by-amino-acid-change-ggd-v1.txt: **4.86K**
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Package Keywords amion-acid, amino-acid-change, constraint, missense-badness-score, blosum-score, granthams-score, amino-acid-score
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Package Dependencies:
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-scores-by-amino-acid-change-ggd-v1
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================================== ====================================

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-transcript-only-features-ensembl-v1/README.rst.txt‎

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.. _`grch37-transcript-only-features-ensembl-v1`:
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grch37-transcript-only-features-ensembl-v1
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==========================================
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|downloads|
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Transcript only features from Ensembl gene sets. All other features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: transcript. Features are in GTF format.
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================================== ====================================
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GGD Package grch37-transcript-only-features-ensembl-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider Ensembl
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Data Version release-75_2-6-14
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-transcript-only-features-ensembl-v1.gtf.gz, grch37-transcript-only-features-ensembl-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-transcript-only-features-ensembl-v1.gtf.gz: **5.04M**, grch37-transcript-only-features-ensembl-v1.gtf.gz.tbi: **207.26K**
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Package Keywords Gene-Features, GTF, Ensembl-GTF, Ensembl-Gene-Set, Annotated-Transcripts, Transcript-Only-Features
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Package Dependencies: gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-transcript-only-features-ensembl-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-transcript-only-features-ensembl-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-transcript-only-features-ensembl-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-transcript-only-features-ensembl-v1

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-transcript-only-features-gencode-v1/README.rst.txt‎

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.. _`grch37-transcript-only-features-gencode-v1`:
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grch37-transcript-only-features-gencode-v1
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==========================================
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|downloads|
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Transcript only features from the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All other features have been removed. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: transcript.
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================================== ====================================
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GGD Package grch37-transcript-only-features-gencode-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider GENCODE
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Data Version release-34_03-24-2020
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-transcript-only-features-gencode-v1.gtf.gz, grch37-transcript-only-features-gencode-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-transcript-only-features-gencode-v1.gtf.gz: **10.20M**, grch37-transcript-only-features-gencode-v1.gtf.gz.tbi: **209.52K**
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Package Keywords Gene-Features, GTF, GENOCDOE-GTF, GENCODE-Gene-Sets, Annotated-Transcripts, Transcript-Only-Features
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Package Dependencies: grch37-chrom-mapping-ucsc2ensembl-ncbi-v1, gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-transcript-only-features-gencode-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-transcript-only-features-gencode-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-transcript-only-features-gencode-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-transcript-only-features-gencode-v1

‎_sources/recipes/genomics/Homo_sapiens/GRCh37/grch37-utr-only-features-ensembl-v1/README.rst.txt‎

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.. _`grch37-utr-only-features-ensembl-v1`:
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grch37-utr-only-features-ensembl-v1
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===================================
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|downloads|
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UTR only features from Ensembl gene sets. All other features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.) UTRs have been designated as 5' UTRs or 3' UTRs based on the coding region and strand of the associated gene .Features include: five_prime_utr, three_prime_utr. Features are in GTF format.
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================================== ====================================
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GGD Package grch37-utr-only-features-ensembl-v1
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Species Homo_sapiens
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Genome Build GRCh37
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GGD Channel ggd-genomics
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Package Version 1
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Recipe Author mjc
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Data Provider Ensembl
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Data Version release-75_2-6-14
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Genomic File Type gtf
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Data file coordinate basing 1-based-inclusive
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Package's Data Files grch37-utr-only-features-ensembl-v1.gtf.gz, grch37-utr-only-features-ensembl-v1.gtf.gz.tbi
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Approximate Size of Each Data File grch37-utr-only-features-ensembl-v1.gtf.gz: **3.97M**, grch37-utr-only-features-ensembl-v1.gtf.gz.tbi: **393.07K**
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Package Keywords Gene-Features, GTF, Ensembl-GTF, Ensembl-Gene-Set, Annotated-Transcripts, UTR-Only-Features, Five-Prime-UTR, Three-Prime-UTR
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Package Dependencies: gsort, htslib, zlib
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Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh37/grch37-utr-only-features-ensembl-v1
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================================== ====================================
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Install with ``--prefix``
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-------------------------
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**Prefix install enabled:** *True*
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Installation
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------------
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.. highlight: bash
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With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::
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ggd install -c ggd-genomics grch37-utr-only-features-ensembl-v1
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.. |downloads| image:: https://anaconda.org/ggd-genomics/grch37-utr-only-features-ensembl-v1/badges/downloads.svg
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:target: https://anaconda.org/ggd-genomics/grch37-utr-only-features-ensembl-v1

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