A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Background

The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets.

Results

Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal.

Conclusions

The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.

[Ambulatory treatment of deep venous thrombosis. From data of a study of 108 patients, an evaluation of its cost and its efficacy]

The study deals with the efficiency and the cost of an ambulatory treatment of deep venous thrombosis by means of Fraxiparine, contention and phlebotonics. 108 patients have been treated. The thrombosis affected the deep veins of the leg in 26 p. cent, the popliteal vein in 9.2 p. cent, the femoropopliteal axis in 19 p. cent as well as superficial thrombosis extended to the depth in 16.6 p. cent. The diagnosis was performed clinically and by ultrasound when phlebography was used in a few cases only (7.4 p. cent). The initial treatment lasted 9.8 days (75 p. cent) 15 days (12 p. cent) and more (12.8 p. cent). Complete re-permeabilization has been noticed in 35.8 p. cent on the 10th day, in 57.5 between the 15th and 30th day. Beside some minor complications 2 recurrences of the thrombosis occurred and 2 patients presented Pulmonary Embolism. They were sent to hospital. The average cost for a treatment was 789 FF for consultation, 1,818 FF for nursing, 1,405 FF for Fraxiparine and 325 FF for contention.

CONCLUSION

hospitalization is sometimes indispensable, sometimes avoidable ... let us make a good choice.