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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 22 months ago by
LauferVA
4.2k • written 22 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 6.5 years ago by
ahmad mousavi
▴ 800
3
votes
2
replies
2.9k
views
Tutorial:
Running fastq_screen on your data
fastqscreen
2.2 years ago by
rohitsatyam102
▴ 860
9
votes
14
replies
3.8k
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 11 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 3.3 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 3.2 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
150
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
88k
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 2.7 years ago by
nhaus
▴ 360
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
88k
0
votes
0
replies
1.2k
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
2.8 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 3 months ago by
MaxF
▴ 120 • written 2.8 years ago by
Kevin Blighe
88k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 15 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
100
votes
106
replies
47k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 5 weeks ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
88k
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
88k
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 5.9 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 3.0 years ago by
cpad0112
21k • written 3.0 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
55
votes
14
replies
93k
views
10 follow
Tutorial:
Using R in Conda
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
rohitsatyam102
▴ 860
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
5.9k
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
88k
8
votes
0
replies
2.8k
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
96k
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
2.4k
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 3.2 years ago by
Kevin Blighe
88k
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 3.2 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 11.5 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 10.6 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
6.9k
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 3.4 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: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
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
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Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
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 caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that versio…
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/
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