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128 results • Page
1 of 3
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Replies
7
votes
1
reply
184
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 8 days ago by
dariober
14k • written 8 days ago by
nhaus
▴ 360
5
votes
5
replies
655
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
Mbofire
• 0 • written 20 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
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 25 days ago by
ATpoint
82k • written 26 days ago by
BioinfGuru
★ 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
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
1
vote
0
replies
219
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
27 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
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 6 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
252
views
Tutorial:
Parsing HMMER output
HMMER
updated 7 weeks ago by
GenoMax
142k • written 7 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 8 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
230
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
578
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
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
655
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 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
ATpoint
82k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
311
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq
MetaTiME
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
264
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
281
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
268
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
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
0
replies
276
views
Tutorial:
Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
6
votes
1
reply
477
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
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
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
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
403
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
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
492
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
Ram
43k • written 10.6 years ago by
Irsan
★ 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
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
2
votes
0
replies
588
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
553
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
4
votes
2
replies
2.9k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 8 months ago by
GenoMax
142k • written 4.0 years ago by
ATpoint
82k
128 results • Page
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Recent Votes
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: genome finishing
Answer: genome finishing
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
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asalimih
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nd48
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★ 1.8k
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Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: Cannot install bwa-mem2 via conda
by
Istvan Albert
100k
The problem is because you are running the ARM based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
[https://www.biostars.org/p/9559284/][1] you could try this [1]: https://www.biostars.org/p/9559284/
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
it's also true that now I only have one pod5 folder, thanks anyway for clarifying the focus of the issue. Yes, they are probably secondary …
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I'm unsure. I will say that looking for [ normalize](https://github.com/search?q=repo%3Atanaylab%2Fmetacells%20normalize&type=code) among t…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: genome finishing
by
nd48
▴ 20
What is the input? Do you have short reads (e.g. illumina 100bp paired reads)? As mentioned already, you already have the consensus i.e. c…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
biology_inform
▴ 50
I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to …
Answer: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Papyrus
★ 2.9k
If you want to plot global accessibility, maybe you would like to plot the ATAC "signal", instead of specific peaks. In a very general mann…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
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: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> I haven't been able to figure out how to generate this plot. show us what you tried and the error messages
Comment: Duplicated reads (IDs) from nanopore sequencing
by
njornet
▴ 20
I think this is the answer but I can't find in the tags info about primary and secondary alignments. I've only found in the flag that the s…
Answer: Add stats to boxplot in R
by
Lélé
• 0
Hi, Have you tried switching the order of the stat_compare_means for the Wilcox with the one for kruskall-Wallis ?
Comment: genome finishing
by
Joe
21k
I may be wrong here so someone feel free to correct me, but I've never noticed a variants file from `SPAdes`, and certainly never used one …
Comment: perseus software (version 1.5.5)
by
Joe
21k
You will need to obtain the software from an official source. I believe Perseus is a paid-for program and as such sharing via the forum wou…
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