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143 results • Page 3 of 3
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Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
replies
1.3k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 11 months ago by 43k • written 5.7 years ago by • 0
0
votes
0
replies
519
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
8 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
1.4k
views
Tutorial: Data Panel In R Commander
R
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
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0
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8.1k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
240
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
815
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 5 months ago by 43k • written 13 months ago by ▴ 10
3
votes
0
replies
734
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
10 months ago by Ming Tommy Tang ★ 3.9k
5
votes
0
replies
1.6k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 10 months ago by 43k • written 16 months ago by ▴ 420
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 11 months ago by 43k • written 6.2 years ago by 22k
1
vote
0
replies
604
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
1.4k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 11 months ago by 43k • written 5.9 years ago by ▴ 340
0
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0
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3.1k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
2.2k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
1
vote
0
replies
271
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
3 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
267
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
0
replies
220
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
8 weeks ago by Novogene ▴ 420
2
votes
0
replies
397
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
334
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
228
views
Tutorial: How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat single-cell ggplot2
3 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
511
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
6 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 10 months ago by 43k • written 6.5 years ago by ★ 2.5k
0
votes
0
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3.6k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
0
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0
replies
1.6k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
7
votes
0
replies
591
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
0
votes
0
replies
307
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
3 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
681
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
2
votes
0
replies
1.5k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 11 months ago by 43k • written 6.2 years ago by ▴ 60
0
votes
0
replies
1.6k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
0
votes
0
replies
2.8k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
2
votes
0
replies
2.1k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.4k
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 11 months ago by 43k • written 6.6 years ago by 35k
0
votes
0
replies
458
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
5 months ago by rohitsatyam102 ▴ 840
6
votes
0
replies
527
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 11 weeks ago by 11k • written 12 weeks ago by ★ 3.9k
0
votes
0
replies
3.6k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
2
votes
0
replies
469
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 5 months ago by • 0 • written 15 months ago by ★ 1.6k
0
votes
0
replies
244
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
1.7k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 11 months ago by 43k • written 6.7 years ago by ▴ 350
0
votes
0
replies
304
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
209
views
Tutorial: Parsing HMMER output
HMMER
updated 4 weeks ago by 141k • written 4 weeks ago by ▴ 140
1
vote
0
replies
320
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
563
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 7 months ago by 43k • written 7 months ago by 161k
143 results • Page 3 of 3
Recent Votes
Comment: alignment result
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)
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Recent Replies
Comment: To get p-values for the TPM by VITALA • 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result by ahmad.sajad4541 • 0
Thank you so much. Should i proceed for annotation step?
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.
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