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8 results • Page 1 of 1
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4
votes
9
replies
2.6k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by • 0
2
votes
0
replies
190
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
13 days ago by Adam ▴ 20
2
votes
3
replies
462
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
15 days ago by Anastasia ▴ 10
362
votes
82
replies
144k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 29 days ago by ▴ 290 • written 11.2 years ago by ★ 4.4k
4
votes
0
replies
865
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
14 days ago by Wubin ▴ 40
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 19 days ago by 43k • written 17 months ago by 47k
1
vote
0
replies
2.1k
views
Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq scRNA-Seq R Batch-Effect
updated 6 days ago by 43k • written 6.9 years ago by ★ 1.1k
6
votes
0
replies
2.6k
views
Tool: Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression batch-effect immunology
updated 6 days ago by 43k • written 7.0 years ago by ▴ 80
8 results • Page 1 of 1
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
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Recent Replies
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment by Scooter ▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host by ZhangYuanfeng • 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed) by Aaliya ▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95？ by Dateline • 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq by Kevin Blighe 87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies by Kevin Blighe 87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue by emmanouil.a ▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package by Pierre Lindenbaum 161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation by Lissa Cruz Saavedra • 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file by swbarnes2 14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model by biochugs • 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed) by Jeremy ▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination by DKA ▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
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