Updating conversion, creating readmes

terminal/biologicalvisualizations

@@ -1,9 +1,9 @@
-                                                          Awesome Biological Visualizations !Awesome (https://awesome.re/badge.svg) (https://awesome.re)
+                                                                       Awesome Biological Visualizations !Awesome (https://awesome.re/badge.svg) (https://awesome.re)
 
 ▐ Interactive visualization of biological data on the web.
 
-Web-based biology-related visualization tools are often scattered across the internet and difficult to discover. They may be found on GitHub, Twitter, or linked from scientific papers. These tools can be very 
-useful to scientists looking to visualize biological data in the context of diseased or healthy humans or model organisms.
+Web-based biology-related visualization tools are often scattered across the internet and difficult to discover. They may be found on GitHub, Twitter, or linked from scientific papers. These tools can be very useful to scientists 
+looking to visualize biological data in the context of diseased or healthy humans or model organisms.
 
 Contents
 - Cancer (#cancer)
@@ -29,8 +29,7 @@
 - iCoMut Beta for FireBrowse (http://firebrowse.org/iCoMut/) - Interactive exploration of mutation rates, mutation signatures, clinical data, gene mutations.
 - MAGI (http://magi.brown.edu) - Visualization and collaborative annotation of genomic aberrations.
 - ExploSig (http://explosig.lrgr.io) - Interactive visualization of mutational signatures and clinical data.
-- Race, Gender, and Age in TCGA (https://www.enpicom.com/visual-lab/tcga-visual-exploration-gender-race-age/) - An interactive visualization of patient gender, race, and age in The Cancer Genome Atlas (TCGA) 
-dataset.
+- Race, Gender, and Age in TCGA (https://www.enpicom.com/visual-lab/tcga-visual-exploration-gender-race-age/) - An interactive visualization of patient gender, race, and age in The Cancer Genome Atlas (TCGA) dataset.
 - OASISPRO (http://tinyurl.com/oasispro) - Omics analysis tool for clinical phenotype prediction.
 - Signal (https://signal.mutationalsignatures.com/) - Mutational signatures extracted from cancer samples and isogenic cell-based experiments.
 - Oncoscape (https://oncoscape.sttrcancer.org/) - An integrated suite of analysis tools for users to explore hypotheses related to molecular and clinical data.
@@ -62,10 +61,8 @@
 Epigenomics
 - Epiviz (http://epiviz.cbcb.umd.edu/4/) - Interactive visual analytics for functional genomics data.
 - GIVe (https://mcf7.givengine.org/) - Epigenome and genome interaction.
-- WashU Epigenome Browser (http://epigenomegateway.wustl.edu/) - Displays many sequencing-based data sets across all or part of the genome, on specific gene sets or pathways, and in the context of their 
-metadata.
-- Clustergrammer CCLE Explorer (https://maayanlab.github.io/CCLE_Clustergrammer/) - Browse relative mRNA expression data for cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) by tissue of origin 
-using Clustergrammer.
+- WashU Epigenome Browser (http://epigenomegateway.wustl.edu/) - Displays many sequencing-based data sets across all or part of the genome, on specific gene sets or pathways, and in the context of their metadata.
+- Clustergrammer CCLE Explorer (https://maayanlab.github.io/CCLE_Clustergrammer/) - Browse relative mRNA expression data for cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) by tissue of origin using Clustergrammer.
 - Peax (https://github.com/Novartis/peax) - Interactive visual pattern exploration in epigenomic data using unsupervised deep representation learning.
 
 Proteomics
@@ -80,9 +77,8 @@
 - Brain mRNA Isoform Atlas (https://isoformatlas.com/) - Visualize cell type signatures of alternative splicing in postnatal development.
 - AlzMap (https://alzmap.org/) - Spatial transcriptomics in Alzheimer's disease.
 - Loom Viewer 
-(http://loom.linnarssonlab.org/dataset/cells/osmFISH/osmFISH_SScortex_mouse_all_cells.loom/NrBEoXQGhYDYoAYLRARigZlRgTDpAtAgFhRnSyg0Wrt1rUVuAHYlCYAOD5AzOo3qNmMAJy8ctaeWAYS0jvNoNqotpO6TSioZgmqmLCTJhNt0ebPCpgAWkQA6
-RJjgkxYxLkwlMrAKxIjr5wbv7~iKxcaLj~0AIkULhK~DAscpwZxGZJ_LIgigB2AK4ANqVKHIbquqi10LVKsgIl5RxyybFQPIGYGAi4yey4PGjDArjsaAgYaBOJaDy4A3i0C4G4EgbUEmiJmIwYmMnm2E0QQA) - Tool for sharing, browsing and visualizing 
-single-cell data stored in the Loom file format.
+(http://loom.linnarssonlab.org/dataset/cells/osmFISH/osmFISH_SScortex_mouse_all_cells.loom/NrBEoXQGhYDYoAYLRARigZlRgTDpAtAgFhRnSyg0Wrt1rUVuAHYlCYAOD5AzOo3qNmMAJy8ctaeWAYS0jvNoNqotpO6TSioZgmqmLCTJhNt0ebPCpgAWkQA6RJjgkxYxLkwlMrAKxIjr5wbv7
+~iKxcaLj~0AIkULhK~DAscpwZxGZJ_LIgigB2AK4ANqVKHIbquqi10LVKsgIl5RxyybFQPIGYGAi4yey4PGjDArjsaAgYaBOJaDy4A3i0C4G4EgbUEmiJmIwYmMnm2E0QQA) - Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
 - TissUUmaps (https://tissuumaps.research.it.uu.se/) - Interactive visualization of large-scale spatial gene expression and tissue morphology data.
 - Giotto Viewer (http://spatialgiotto.rc.fas.harvard.edu/giotto.viewer.html) - A web-based visualization package for spatial transcriptomic data.
 
@@ -112,8 +108,8 @@
 - Avivator (http://avivator.gehlenborglab.org/) - A lightweight "batteries-included" WebGL viewer for remote imaging data in Bio-Formats Zarr or OME-TIFF format.
 
 Connectomics
-- neuroglancer (https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/kc_apl_mpn1.json) - Tool for visualization of highly detailed maps of
-neuronal connectivity in the fly brain.
+- neuroglancer (https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/kc_apl_mpn1.json) - Tool for visualization of highly detailed maps of neuronal connectivity in
+the fly brain.
 - Allen Mouse Brain Connectivity Atlas (http://connectivity.brain-map.org/) - A high-resolution map of neural connections in the mouse brain.
 - FlyWire (https://flywire.ai/) - A human-AI collaboration to map the fly connectome.