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412 results • Page
1 of 9
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Replies
7
votes
1
reply
196
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 10 days ago by
dariober
14k • written 10 days ago by
nhaus
▴ 360
5
votes
5
replies
666
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 14 days ago by
Mbofire
• 0 • written 22 days ago by
Ming Tommy Tang
★ 3.9k
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
22 days ago by
Kevin Blighe
88k
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 27 days ago by
ATpoint
82k • written 28 days ago by
BioinfGuru
★ 1.7k
7
votes
3
replies
3.0k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 28 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
1
vote
0
replies
221
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
29 days ago by
Novogene
▴ 420
87
votes
24
replies
24k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 29 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
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 7 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
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
Ram
43k • written 6.2 years ago by
Kevin Blighe
88k
0
votes
0
replies
258
views
Tutorial:
Parsing HMMER output
HMMER
updated 8 weeks ago by
GenoMax
142k • written 8 weeks ago by
I0110
▴ 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
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 9 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
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
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
2
votes
0
replies
233
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
11 weeks ago by
Novogene
▴ 420
3
votes
0
replies
252
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
11 weeks ago by
Novogene
▴ 420
6
votes
0
replies
584
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by
zx8754
11k • written 3 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
347
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
668
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
3
votes
2
replies
578
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by
ATpoint
82k • written 4 months ago by
Julia Ma
▴ 120
2
votes
1
reply
477
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq
space
clustering
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
313
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq
MetaTiME
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
268
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq
SCSA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
287
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq
SCSA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
0
replies
309
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq
SCSA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
305
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
0
replies
372
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
273
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
310
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
353
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
581
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
2
votes
0
replies
442
views
Tutorial:
Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
0
replies
294
views
Tutorial:
Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
1
reply
376
views
Tutorial:
Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING
ppi
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
2
votes
3
replies
648
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
6
votes
1
reply
486
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
294
views
Tutorial:
Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python
RNA-seq
batch-correction
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
GenoMax
142k • written 3.8 years ago by
lavinia.gordon
▴ 160
1
vote
0
replies
373
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
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 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
zhuanggj706
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
0
votes
0
replies
411
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 5 months ago by
Ram
43k • written 5 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
356
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
394
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
497
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
773
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
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
1
vote
0
replies
555
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
ha2606
• 0 • written 6.4 years ago by
vimalkvn
▴ 320
2
votes
0
replies
594
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 8 months ago by
Ram
43k • written 8 months ago by
Pierre Lindenbaum
161k
0
votes
1
reply
559
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 8 months ago by
ATpoint
82k • written 8 months ago by
JC
▴ 30
412 results • Page
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Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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