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3
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Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 11 hours ago by 43k • written 2 days ago by ★ 3.9k
76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
2 days ago by Kevin Blighe 87k
5
votes
13
replies
1.2k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 6 days ago by 82k • written 7 days ago by ★ 1.7k
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 8 days ago by 6.4k • written 15 months ago by ▴ 130
1
vote
0
replies
177
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
8 days ago by Novogene ▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 9 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 29 days ago by 100k • written 8.2 years ago by 43k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 4 weeks ago by 43k • written 6.2 years ago by 87k
0
votes
0
replies
215
views
Tutorial: Parsing HMMER output
HMMER
updated 5 weeks ago by 141k • written 5 weeks 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 5 weeks ago by ▴ 30 • written 7.6 years ago by ▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 weeks ago by ★ 1.2k • written 5.1 years ago by 16k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 6 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
206
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
8 weeks ago by Novogene ▴ 420
3
votes
0
replies
223
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
8 weeks ago by Novogene ▴ 420
6
votes
0
replies
534
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 12 weeks ago by 11k • written 12 weeks ago by ★ 3.9k
0
votes
0
replies
312
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
5
replies
612
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
2
replies
531
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 3 months ago by ▴ 120
2
votes
1
reply
404
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
288
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
243
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
245
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
273
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
269
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
332
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
232
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
277
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
310
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
537
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
404
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
246
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
1
reply
328
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
3
replies
564
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
6
votes
1
reply
434
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
255
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 3 months 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 4 months ago by 141k • written 3.7 years ago by ▴ 160
1
vote
0
replies
341
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 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 8 months ago by ★ 3.9k
16
votes
3
replies
4.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.1 years ago by • 0 • written 3.6 years ago by 3.2k
0
votes
0
replies
360
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
322
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
368
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 850
0
votes
0
replies
461
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
5 months ago by rohitsatyam102 ▴ 850
0
votes
4
replies
728
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
515
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
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.3 years ago by ▴ 320
2
votes
0
replies
566
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
529
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 7 months ago by 82k • written 7 months ago by ▴ 30
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 4.0 years ago by 82k
411 results • Page 1 of 9
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A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Scholar to Alex Reynolds 35k
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Recent Replies
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq by dsull ★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by ATpoint 82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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