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412 results • Page 1 of 9
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7
votes
1
reply
182
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 7 days ago by 14k • written 7 days ago by ▴ 360
5
votes
5
replies
654
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 11 days ago by • 0 • written 20 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
20 days ago by Kevin Blighe 88k
5
votes
13
replies
1.9k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 24 days ago by 82k • written 25 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 26 days ago by 6.4k • written 16 months ago by ▴ 130
1
vote
0
replies
219
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
26 days ago by Novogene ▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 27 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 7 weeks ago by 43k • written 6.2 years ago by 88k
0
votes
0
replies
251
views
Tutorial: Parsing HMMER output
HMMER
updated 7 weeks ago by 142k • written 7 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 8 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 9 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
229
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
11 weeks ago by Novogene ▴ 420
3
votes
0
replies
249
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
11 weeks ago by Novogene ▴ 420
6
votes
0
replies
576
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
343
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
654
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
574
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 4 months ago by ▴ 120
2
votes
1
reply
464
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
1
reply
310
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
263
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
279
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
303
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
301
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
367
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
267
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
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
304
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
348
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 4 months ago by ▴ 120
0
votes
1
reply
573
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 4 months ago by ▴ 120
2
votes
0
replies
436
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
276
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
1
reply
368
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
3
replies
638
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
477
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
286
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 3.8 years ago by ▴ 160
1
vote
0
replies
368
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
402
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 43k • written 5 months ago by ★ 3.9k
1
vote
0
replies
353
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
391
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 860
0
votes
0
replies
491
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 860
0
votes
4
replies
767
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
34k
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
547
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
587
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 8 months ago by 43k • written 8 months ago by 161k
0
votes
1
reply
553
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
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
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Recent Replies
Comment: RNA seq analysis by prifa ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype 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…
Answer: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by melissa.joubert • 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data? by Arton • 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax? by mbrav005 • 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon by sansan_96 ▴ 90
..........
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
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