fungenomics/braindex

Issues

• Height of dendrogram bubble plot dependent on number of genes in file

  #68 opened 8 months ago by bhavyaac
  0

• Heatmap not being produced

  #67 opened 8 months ago by bhavyaac
  0

• Remove sidebar input options on the landing page

  #59 opened a year ago by bhavyaac
  0

• Switch expression table to display Pct1 (detection rate in cluster)

  #66 opened a year ago by bhavyaac
  1

• Add gene specificity score analysis

  #34 opened a year ago by sjessa
  1

• Add Google Analytics for tracking accession stats

  #30 opened a year ago by sjessa
  2

• Solve bookmarking bug: store file input genes in variable with text input genes

  #63 opened 3 years ago by bhavyaac
  0

• Allow individual gene selection in dimensionality reduction tabs

  #62 opened 3 years ago by bhavyaac
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• Add download functionality for marker tables

  #58 opened 3 years ago by bhavyaac
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• Show cluster information in table without requiring gene input

  #57 opened 3 years ago by bhavyaac
  0

• Add ability to click on a cluster in expression table & pull up info/markers

  #8 opened 3 years ago by sjessa
  11

• Add citation, methods, contributors, code info

  #27 opened 3 years ago by sjessa
  1

• Add landing page and tour

  #31 opened 3 years ago by sjessa
  5

• Add new column label bars to heatmap

  #50 opened 3 years ago by bhavyaac
  2

• Export contents unrelated to Shiny from server.R to functions.R

  #55 opened 3 years ago by bhavyaac
  0

• Explain differences between dimensionality reductions, scaling

  #6 opened 5 years ago by sjessa
  1

• Implement nested cell type selection in heatmap tab

  #49 opened 3 years ago by bhavyaac
  1

• Adjust alignment of the gene labels with the dendrogram bubble plots

  #39 opened 3 years ago by bhavyaac
  0

• (accidental issue, please delete)

  #54 opened 3 years ago by bhavyaac
  0

• Subset & visualize single cells based on gene expression thresholds

  #53 opened 3 years ago by bhavyaac
  0

• Alter heatmap & histogram label positioning for increased readability

  #46 opened 3 years ago by bhavyaac
  1

• Add plot download functionality to ranked clusters & heatmap tabs

  #47 opened 3 years ago by bhavyaac
  0

• Allow user to select between input genes in ranked clusters tab

  #48 opened 3 years ago by bhavyaac
  0

• Refactor code to use new timepoints dataset for existing app functions

  #11 opened 4 years ago by bhavyaac
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• Improve input validation to detect typos & synonymous genes

  #51 opened 3 years ago by bhavyaac
  0

• Deal with excessive table width: horizontal scroll, freeze column(s), move search box

  #40 opened 3 years ago by bhavyaac
  2

• Fix alignment of bubble plot w/ dendrogram for long gene names

  #7 opened 4 years ago by sjessa
  1

• Change table text to white when background colour is dark

  #32 opened 3 years ago by bhavyaac
  2

• Reorder gene columns in expression table tab to match user input

  #16 opened 3 years ago by bhavyaac
  0

• Handle all-zero (?) expression rescaling in heatmap

  #45 opened 3 years ago by bhavyaac
  1

• Add ability to cluster cell types based on mean expression of input genes

  #21 opened 3 years ago by sjessa
  7

• Allow .txt files for gene list upload

  #42 opened 3 years ago by bhavyaac
  0

• Allow identification of active/specific TFs for a given cluster

  #23 opened 3 years ago by sjessa
  0

• Make all TFs in annotation available for searching

  #26 opened 3 years ago by sjessa
  0

• Allow user to upload a file containing a list of genes to interrogate

  #17 opened 3 years ago by bhavyaac
  8

• Add visualization(s) of clusters ranked by mean expression of input gene

  #20 opened 3 years ago by sjessa
  7

• Show number of cells expressing the gene in timecourse tooltip

  #19 opened 3 years ago by bhavyaac
  3

• Extract input validation into a function (currently duplicated code)

  #37 opened 3 years ago by bhavyaac
  0

• Display buttons above the timecourse plot to "scroll" between gene inputs

  #38 opened 3 years ago by bhavyaac
  3

• Add ability to bookmark URL to capture current state of the app (using a button)

  #28 opened 3 years ago by sjessa
  2

• For 2D gene plotting, fix the case when a gene has 0 expression in all samples in one region

  #35 opened 3 years ago by sjessa
  4

• Implement more granular reactivity in joint expression tabs

  #9 opened 4 years ago by bhavyaac
  0

• Add ability to click on a cluster in dim red & pull up top active/specific TFs

  #25 opened 3 years ago by sjessa
  0

• For plotting in 2D space, fix the case where gene has a value of 0 in all cells of a given sample

  #10 opened 4 years ago by sjessa
  0

• Fix bubble plot label & ordering for genes such as 4732440D04Rik

  #14 opened 4 years ago by bhavyaac
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• Plot mean expression (over selected genes) in a separate bubble plot

  #18 opened 4 years ago by bhavyaac
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• Implement interactivity for heatmaps

  #29 opened 4 years ago by sjessa
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• Add quantification of user input gene lists within TF regulons

  #22 opened 4 years ago by sjessa
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• Add searchable analyses of network/regulon changes over timecourse

  #24 opened 4 years ago by sjessa
  0

• Add option for table export for Clusters app

  #5 opened 4 years ago by sjessa
  0