spreadsheet tools alternative
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5.0 years ago
sacha ★ 2.4k

Hi,

As you know, Excel is not safe to do bioinformatics stuff because it changes your data. https://www.ncbi.nlm.nih.gov/pubmed/15214961.
I guess biologist can disable those features, but it seems to hard.

Do you know other simple spreadsheet software which can be used by biologist ? Something like : TSV/CSV editor ?

excel spreadsheet gui • 1.8k views
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This is not a fair question. You are saying it's too hard to adjust some settings in Excel. Learning how to use a completely new software tool will not be easier.

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MS Excel does not change data. You need to format the excel cells as per your format.

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Renesh's comment is not correct. Try the following: Open a worksheet. Type "MAR7". You'll see "7-Mar" as Excel formats your text as a date. Now correct the formatting to "text" (Format|Cells). You will see "7-Mar" become a number. On my Macintosh it's 42801. There is no way to recover the original text "MAR7". The data are changed.

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As I said, you need to format first the cells to type your data as you need. For example, select the column and change the formatting to Text. Now, type MAR7 and it will be displayed exactly as MAR7

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Now imagine teaching that habit to many thousands of biologists around the world who still use Excel.

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As with everything, you just have to know how to use it properly. If you want to preserve your data exactly as it is, open a blank Excel sheet, format all cells as text, and then paste your data into it as plain text. This prevents Excel from doing any automatic changes.

Unfortunately, however, even data on the Nature server that's associated with published work has these formatting issues.

Excel is a very powerful tool that anyone should be grateful for having. That said, as I get more skilled with awk and sed, I find that I need to use Excel less and less. In fact, I have not used it in the last year.

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5.0 years ago

http://www.knime.org workbench

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5.0 years ago

Unless you have regulatory issues to be worried about, you could use Google Sheets: https://www.google.com/sheets/about/

One advantage to doing work in the cloud with a tool like Google Sheets is that this makes your data easily shared with colleagues, and you can do collaborative and concurrent editing wherever you have a web browser and network connection available to you.

A disadvantage is that this makes your data easily shared with people who aren't your colleagues — as well as with Google, who have financial affiliations with companies like 23andMe etc. So keep this in mind if you are working with medical or proprietary data.

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Yes, and those online Word processors, etc, appear to be getting better over time. I used Word online completely for the first time last week (via my Outlook account). As you've implied, though, for things like clinical data, it may actually be against the law to host such data on a third-party server. Regulations differ per health system and nation, though.

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5.0 years ago
sacha ★ 2.4k

Just found : http://csved.sjfrancke.nl/

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I have not tried it myself but perhaps google sheets is another easy option without requiring another program install.

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5.0 years ago

GraphPad Prism is good for statistics and nice plots

Some stuff may also be done in Galaxy, depends on the question that needs to be addressed, but Galaxy basically give GUI-based access to many of the bash functions, such as cut, sed, even awk-like stuff.

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GraphPad Prism is commercial software and requires a license purchase.

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so does Excel, no? If the question implied only free solutions I missed that.

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I generally like to know if software being mentioned/recommended on Biostars is freely available or requires a purchase. That was the reason I was only making a note that Prism is not free software.

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5.0 years ago
h.mon 34k

The most obvious Excel replacement is LibreOffice Calc. Two alternatives are pyspread and Tad.

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Are they known not to change gene names :)

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I didn't test extensively, but as far as I noticed the genes usually changed by MSExcel (MARCH5, SEPT10, etc) are untouched. For me, they also have the advantage of not messing with scientific notation and decimals - which may happen due to some localization issue due to differences between my language locales and scietific standards.

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I think that LibreOffice Calc is less forgiving that Excel, but in that sense it is better for people like us who need to know all changes that are happening to our data! I have been using Calc for the past year and I would say that it gets better when you learn how to use it.

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5.0 years ago
igor 13k

A lean and simple (only 218 bytes!) spreadsheet app: http://xem.github.io/sheet/

Free, open source, and no extra crud to mess up dates!

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5.0 years ago
Renesh ★ 2.1k

MS Excel is not a good tool for data analysis unless you have small-scale data. To manipulate tables efficiently and considering large-scale datasets, it is always better to use databases like MySQL or Psql which are open source and easy to use. You can also manipulate these databases through scripting and statistical languages like Python, R etc.

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I m just wondering if it's possible to index a tabular text file to have random access ...

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Yes you can index tabular files in MySQL or Psql

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I m stupid... tabix do that !

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and tribble (gatk/picard=

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Greate! Let's look which gui viewer support index file to load and edit large dataset

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