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139 results • Page 1 of 3
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85
votes
23
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 2 days ago by • 0 • written 3.5 years ago by 3.2k
49
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 18 days ago by 100k • written 8.1 years ago by 43k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 20 days ago by 43k • written 6.2 years ago by 87k
0
votes
0
replies
191
views
Tutorial: Parsing HMMER output
HMMER
updated 24 days ago by 141k • written 24 days ago by ▴ 140
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 28 days ago by ▴ 30 • written 7.5 years ago by ▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 4 weeks ago by ★ 1.2k • written 5.1 years ago by 16k
46
votes
13
replies
14k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 5 weeks ago by • 0 • written 3.5 years ago by 3.2k
2
votes
0
replies
189
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
7 weeks ago by Novogene ▴ 410
3
votes
0
replies
205
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
7 weeks ago by Novogene ▴ 410
6
votes
0
replies
487
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 10 weeks ago by 11k • written 10 weeks ago by ★ 3.9k
0
votes
0
replies
294
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
12 weeks ago by Ming Tommy Tang ★ 3.9k
1
vote
5
replies
579
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 120
3
votes
2
replies
505
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 81k • written 3 months ago by ▴ 120
2
votes
1
reply
376
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
1
reply
274
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
232
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
0
votes
0
replies
229
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
254
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
0
votes
0
replies
254
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
306
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
214
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
259
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
0
votes
0
replies
285
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
1
reply
519
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
0
replies
371
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 12 weeks ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
228
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 12 weeks ago by 43k • written 3 months ago by ▴ 120
1
vote
1
reply
301
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 12 weeks ago by 43k • written 3 months ago by ▴ 120
2
votes
3
replies
527
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 12 weeks ago by 43k • written 3 months ago by ▴ 120
6
votes
1
reply
411
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 12 weeks ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
228
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 12 weeks ago by 43k • written 3 months ago by ▴ 120
39
votes
16
replies
36k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 3 months ago by 141k • written 3.7 years ago by ▴ 160
1
vote
0
replies
326
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
3 months ago by Ming Tommy Tang ★ 3.9k
3
votes
3
replies
1.1k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 3 months ago by ▴ 40 • written 7 months ago by ★ 3.9k
0
votes
0
replies
339
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 4 months ago by 43k • written 4 months ago by ★ 3.9k
1
vote
0
replies
309
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
357
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
4 months ago by rohitsatyam102 ▴ 840
0
votes
0
replies
449
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
5 months ago by rohitsatyam102 ▴ 840
0
votes
4
replies
703
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
90
votes
48
replies
33k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 5 months ago by 43k • written 10.5 years ago by ★ 7.8k
1
vote
0
replies
497
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
5 months ago by Ming Tommy Tang ★ 3.9k
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 months ago by • 0 • written 6.3 years ago by ▴ 320
2
votes
0
replies
553
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
0
votes
1
reply
517
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 7 months ago by 81k • written 7 months ago by ▴ 30
4
votes
2
replies
2.8k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 3.9 years ago by 81k
0
votes
0
replies
660
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
7 months ago by Ming Tommy Tang ★ 3.9k
14
votes
3
replies
20k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 8 months ago by ▴ 30 • written 7.0 years ago by ★ 1.6k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
0
votes
0
replies
509
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
9
votes
4
replies
5.4k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months ago by Hamid Ghaedi 3.2k
7
votes
0
replies
585
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
139 results • Page 1 of 3
Recent Votes
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
Tumour purity and ploidy estimation
Answer: Can I perform scRNAseq data integration without loosing features?
Answer: bcftools select sites with multiple combinatio ns of FILTER column
Comment: How does FindNeighbors() and FindClusters() related and work?
Answer: Deseq2 : Paired analysis or otherwise
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Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the by Spring • 0
Thank you very much!
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the by Spring • 0
Thank you so much! If the 10x Chromium protocol is not used, should the processing be done with HISAT2, FeatureCounts, and so on?
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the by fracarb8 ★ 1.6k
For the paper, they used the `indrop` pipeline (https://github.com/indrops/indrops), and you should have a look at it, and try to run with …
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the by ATpoint 81k
CellRanger is specific for 10x Chromium. I did not check the details of this single-cell platform so I recommend to see what papers that us…
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Pierre Lindenbaum 161k
<!-- The New York Times is an American daily newspaper based in New York City. The New York Times covers domestic, national, and internatio…
Comment: Tumour purity and ploidy estimation by Lloyd98 • 0
Hello bp22, I'm in the same situation as you, I have Whole Exome Sequencing data for tumour samples only, with no normal samples. I haven'…
Comment: Ensembl gene id conversion by naveedhasan2000 • 0
I actually have a list of ensembl ids generated while doing a read count using htseq, i used the reference genome from ensembl. I then trie…
Comment: Odd results with BLAST remote by b.contreras.moreira ▴ 150
See https://www.biostars.org/p/9486493 and parameter `-max_hsps 1`
Answer: WGCNA network from Adjacency or TOM matrix by andres.firrincieli 3.6k
Since the module detection is performed on the TOM, you should go for the TOM.
Answer: Error in edgeR/Deseq2 Analysis by kuttibiotech2009 ▴ 30
The error message you're encountering suggests that there might be duplicate row names in your input data file. check it once again whether…
Comment: Getting marker genes for cell types by orzrzlyo ▴ 20
Thank you! Also, cell typist would successfully identify the above cell types, however, they seemed to be in a pretrained or pre-organized …
Answer: Getting marker genes for cell types by LChart 3.9k
It seems strange that celltypist would not identify these major cell classes -- you should double check your data quality. For the marker l…
Answer: gene body coverage with RSeqQC by jkim ▴ 170
http://qualimap.conesalab.org/doc_html/index.html Never tried rseqc, but qualimap provides a gene body coverage plot also.
Comment: How to get the reference panel sites for TOPMed hg37 and 38 by bk11 ★ 2.3k
You can simply impute your genotyped data in TOPMed server. In that way you do not have to deal with downloading the reference panels (not …
Answer: Using adonis to include a random effect by LChart 3.9k
> why the first model doesn't have stats for both variables? Your variables are multicollinear. This will always be true if you have mul…
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