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| -rw-r--r-- | issues/add-bulklmm-feature.gmi | 14 | ||||
| -rw-r--r-- | issues/add-pluto-notebooks.gmi | 23 | ||||
| -rw-r--r-- | issues/fix-genotype-filename-HSNIH-Palmer.gmi | 30 |
3 files changed, 67 insertions, 0 deletions
diff --git a/issues/add-bulklmm-feature.gmi b/issues/add-bulklmm-feature.gmi new file mode 100644 index 0000000..8fdd784 --- /dev/null +++ b/issues/add-bulklmm-feature.gmi @@ -0,0 +1,14 @@ +## BulkLMM integration + +## Tags + +* assigned: pjotrp +* type: feature +* priority: high + +## Description + +Integrate BulkLMM in GeneNetwork. The first step is to test the command line interface to BulkLMM in GeneNetwork using the BulkLMMSysimage. +The BulkLMMSysimage files provides instructions for generating the BulkLMM.jl sysimage,along with the code for the command-line functions. + +=> https://github.com/senresearch/BulkLMMSysimage BulkLMMSysimage files
\ No newline at end of file diff --git a/issues/add-pluto-notebooks.gmi b/issues/add-pluto-notebooks.gmi new file mode 100644 index 0000000..7c4c649 --- /dev/null +++ b/issues/add-pluto-notebooks.gmi @@ -0,0 +1,23 @@ +## Add Pluto Notebooks + +## Tags + +* assigned: pjotrp +* type: feature +* priority: high + +## Description + +Host Pluto Notebooks in GeneNetwork. As a proof of concept, we host: + +=> https://notebooks.one/ notebooks.one + +We used the package PlutoSliderServer.jl: + +=> https://github.com/JuliaPluto/PlutoSliderServer.jl PlutoSliderServer.jl + +See also our deployment repo for notebooks.one: + +=> https://github.com/GregFa/visuals/tree/testing + +Considering its capabilities, PlutoSliderServer.jl could potentially serve as a viable solution for hosting Pluto Notebooks on GeneNetwork. diff --git a/issues/fix-genotype-filename-HSNIH-Palmer.gmi b/issues/fix-genotype-filename-HSNIH-Palmer.gmi new file mode 100644 index 0000000..246b230 --- /dev/null +++ b/issues/fix-genotype-filename-HSNIH-Palmer.gmi @@ -0,0 +1,30 @@ +## Fix genotype filename HSNIH-Palmer + +## Tags + +* assigned: pjotrp +* type: bug fix +* priority: high + +## Description + + +When using the Rest API to get the groups for "rat", it mentions the group HSNIH-Palmer. +But the REST API to obtain the geno file(http://gn2.genenetwork.org/api/v_pre1/gentotypes/HSNIH-Palmer.geno) failed. +The file of HSNIF-Palmer has actually a different name from what is expected; we have to use "HSNIH-Palmer_true" instead. +On GeneNetwork website, the following query does not return results from the search. + +Dataset try to access: HSNIH-Palmer + +Issues with genotyped data: +Used this query: + +Species: Rat + +Group: NIH Heterogeneous Stock (Palmer) + +Type: DNA Markers and SNPs + +Dataset: HSNIH-Palmer Genotypes + +Get Any: * |