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412 results • Page 1 of 9
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7
votes
1
reply
153
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 2 days ago by 14k • written 2 days ago by ▴ 360
5
votes
5
replies
619
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 5 days ago by • 0 • written 14 days ago by ★ 3.9k
76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
14 days ago by Kevin Blighe 87k
5
votes
13
replies
1.7k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 19 days ago by 82k • written 20 days ago by ★ 1.7k
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 20 days ago by 6.4k • written 16 months ago by ▴ 130
1
vote
0
replies
204
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
21 days ago by Novogene ▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 21 days ago by • 0 • written 3.6 years ago by 3.2k
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 6 weeks ago by 100k • written 8.2 years ago by 43k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 weeks ago by 43k • written 6.2 years ago by 87k
0
votes
0
replies
240
views
Tutorial: Parsing HMMER output
HMMER
updated 6 weeks ago by 142k • written 6 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 7 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 8 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 8 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
223
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
10 weeks ago by Novogene ▴ 420
3
votes
0
replies
243
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
10 weeks ago by Novogene ▴ 420
6
votes
0
replies
559
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by 11k • written 3 months ago by ★ 3.9k
0
votes
0
replies
334
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
642
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
560
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
444
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
306
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
259
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
269
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
296
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
290
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
359
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
257
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
296
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
338
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
562
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
423
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
265
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
354
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
619
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
6
votes
1
reply
465
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
273
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 4 months ago by ▴ 120
39
votes
16
replies
37k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 months ago by 142k • written 3.7 years ago by ▴ 160
1
vote
0
replies
359
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
16
votes
3
replies
4.4k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.2 years ago by • 0 • written 3.6 years ago by 3.2k
0
votes
0
replies
385
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 4 months ago by 43k • written 5 months ago by ★ 3.9k
1
vote
0
replies
342
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
384
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
481
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 850
0
votes
4
replies
754
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 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 6 months ago by 43k • written 10.6 years ago by ★ 7.8k
1
vote
0
replies
533
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
579
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
547
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
412 results • Page 1 of 9
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Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
A: Insert Size And Fragment Size ?
Answer: samtools 1.0 'index' : CSI index vs BAI index ?
Comment: Nextflow and self-made pipelines opinion
Comment: Nextflow and self-made pipelines opinion
What is Deepvariant default filtering values ?
Answer: Nextflow: how to get the process work dir, within the process
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Recent Awards • All
Scholar to tim.booth ▴ 40
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Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 40
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length by Pierre Lindenbaum 161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file by sainavyav22 • 0
Here you go. ***1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 1008Tumo…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
Comment: Help with Biopython for Beginner by GenoMax 142k
> That turns it into a mess of paragraphs See above. Select (highlight with mouse) the part you want to represent as `code` and then click…
Comment: Help with Biopython for Beginner by cput • 0
That turns it into a mess of paragraphs, but if it truly is more productive thanks for the tip!
Comment: Presence of unknown sites in ANNOVAR output file by Ram 43k
Please show us your full annovar command line.
Comment: input file for alternative splicing in rmats in linux by Ram 43k
I've done what I can to make your post more professional. Stick to outlining your problem, personal pleas do not really belong on a profess…
Comment: Contig assembly task, errors by rackbersingh • 0
Hi Phillip, Thanks for providing an answer and clearing up some confusion, looking into what you said about older assemblers reverse comp…
Comment: How to analyze Infinium Mouse Methylation BeadChip array data? by Tawny ▴ 180
Did you get this figured out? I am having the same error in R.
Answer: JASPAR2024_getMatrixSet error by Raghad • 0
Try this: ```r #Read the motifs library(JASPAR2024) library(TFBSTools) jaspar <- JASPAR2024() sq24 <- RSQLite::dbConnect(RSQLite::SQLite…
Answer: How to convert normalized BigWig file to count matrix? by ATpoint 82k
It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
Comment: bcftools - reducing to "sites-only"? by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: bcftools - reducing to "sites-only"? by Matthew • 0
Thank you Pierre! Not sure why I didn't notice that (I should have)
Comment: How to convert normalized BigWig file to count matrix? by Pierre Lindenbaum 161k
bigwig is chrom/start/end/value . what kind of matrix do you want ?
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