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412 results • Page
3 of 9
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2
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1
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61k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 21 months ago by
LauferVA
4.2k • written 21 months ago by
kodwings
▴ 20
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.9 years ago by
egeulgen
★ 1.3k
87
votes
2
replies
59k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Eric Normandeau
11k
16
votes
5
replies
13k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 14 months ago by
Ram
43k • written 6.4 years ago by
ahmad mousavi
▴ 800
3
votes
2
replies
2.9k
views
Tutorial:
Running fastq_screen on your data
fastqscreen
2.1 years ago by
rohitsatyam102
▴ 850
9
votes
14
replies
3.7k
views
6 follow
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 18 months ago by
Angelina_G
▴ 10 • written 2.2 years ago by
thehung92phuyen
▴ 40
76
votes
14
replies
16k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 15 months ago by
Ram
43k • written 11.0 years ago by
Medhat
9.7k
35
votes
13
replies
14k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 2.3 years ago by
liorglic
★ 1.4k • written 2.6 years ago by
Istvan Albert
100k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 10 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
16
votes
9
replies
7.1k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 23 months ago by
dk0319
▴ 70 • written 2.4 years ago by
Barry Digby
★ 1.3k
0
votes
0
replies
11k
views
Tutorial:
Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter
Python
pattern
2.3 years ago by
Wayne
★ 2.0k
12
votes
4
replies
5.4k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 15 months ago by
Ram
43k • written 3.2 years ago by
garden_giessen
▴ 130
30
votes
10
replies
82k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 14 months ago by
Ram
43k • written 3.1 years ago by
Nitin Narwade
★ 1.6k
46
votes
6
replies
25k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.3 years ago by
cameron.cowan
▴ 50 • written 3.1 years ago by
rpolicastro
13k
149
votes
70
replies
51k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.5 years ago by
Kevin Blighe
87k
15
votes
2
replies
2.1k
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 19 months ago by
brunobsouzaa
▴ 830 • written 2.6 years ago by
nhaus
▴ 340
196
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 16 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
6
votes
2
replies
1.6k
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
2.7 years ago by
Kevin Blighe
87k
0
votes
0
replies
1.2k
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
2.7 years ago by
mo
• 0
3
votes
1
reply
3.4k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 12 weeks ago by
MaxF
▴ 120 • written 2.8 years ago by
Kevin Blighe
87k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 14 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
99
votes
106
replies
47k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 29 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
0
votes
0
replies
1.1k
views
Tutorial:
Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation
bioimaging
SLURM
health
2.9 years ago by
Erin Haskell | ELIXIR
▴ 470
1
vote
0
replies
1.3k
views
Tutorial:
Slurm and parallelization
slurm
2.9 years ago by
Juke34
8.6k
1
vote
0
replies
1.3k
views
Tutorial:
How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo
cytoscape
2.9 years ago by
Pratik
★ 1.0k
14
votes
1
reply
3.1k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 2.9 years ago by
jared.andrews07
★ 16k • written 2.9 years ago by
Kevin Blighe
87k
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 14 months ago by
Ram
43k • written 5.8 years ago by
ATpoint
82k
4
votes
0
replies
1.2k
views
Tutorial:
Long Read Genome Assembly Video Series
long-read
genome-assembly
2.9 years ago by
pbpanigrahi
▴ 420
0
votes
1
reply
1.1k
views
Tutorial:
Add Customized Filters in GDC
gdc
updated 2.9 years ago by
cpad0112
21k • written 2.9 years ago by
Zhenyu Zhang
★ 1.2k
12
votes
20
replies
14k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 14 months ago by
Ram
43k • written 4.9 years ago by
jared.andrews07
★ 16k
4
votes
2
replies
2.5k
views
Tutorial:
Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0
beagle
updated 14 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
54
votes
14
replies
92k
views
10 follow
Tutorial:
Using R in Conda
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
rohitsatyam102
▴ 850
99
votes
16
replies
34k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 14 months ago by
Ram
43k • written 7.8 years ago by
Jean-Karim Heriche
27k
23
votes
2
replies
5.8k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 20 months ago by
eggrandio
▴ 40 • written 3.1 years ago by
Juke34
8.6k
32
votes
6
replies
12k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 14 months ago by
Ram
43k • written 4.0 years ago by
Kevin Blighe
87k
8
votes
0
replies
2.7k
views
Tutorial:
Pipes in R: An introduction and some advanced tips and tricks.
R
3.1 years ago by
rpolicastro
13k
239
votes
176
replies
95k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.8 years ago by
TriS
★ 4.7k
6
votes
0
replies
2.3k
views
Tutorial:
data.frames in R: How vectorization can save you time and heartache
R
3.1 years ago by
rpolicastro
13k
8
votes
1
reply
1.4k
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta
awk
updated 14 months ago by
Ram
43k • written 3.1 years ago by
Kevin Blighe
87k
22
votes
10
replies
7.1k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 14 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
12
votes
2
replies
1.3k
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
updated 14 months ago by
Ram
43k • written 3.1 years ago by
rpolicastro
13k
149
votes
35
replies
62k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 14 months ago by
Ram
43k • written 11.4 years ago by
vijay
★ 1.6k
16
votes
7
replies
16k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 14 months ago by
Ram
43k • written 4.9 years ago by
atakanekiz
▴ 310
298
votes
33
replies
109k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
6
votes
2
replies
5.0k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by
GenoMax
142k
11
votes
0
replies
6.8k
views
Tutorial:
Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 14 months ago by
Ram
43k • written 3.3 years ago by
GenoMax
142k
10
votes
0
replies
5.0k
views
Tutorial:
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 14 months ago by
Ram
43k • written 3.3 years ago by
GenoMax
142k
11
votes
1
reply
2.7k
views
Tutorial:
Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 14 months ago by
Ram
43k • written 3.3 years ago by
Mensur Dlakic
★ 27k
40
votes
9
replies
11k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 14 months ago by
Ram
43k • written 10.1 years ago by
Ahill
★ 1.9k
0
votes
1
reply
3.0k
views
Tutorial:
Getting the lineage of an organism from NCBI taxonomy data
biosql
python
taxonomy
updated 14 months ago by
Ram
43k • written 5.8 years ago by
vimalkvn
▴ 320
412 results • Page
3 of 9
Recent Votes
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
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Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq
by
robert.flynn.21
• 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
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