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348 results • Page
1 of 7
Sort: Rank
Rank
Views
Votes
Replies
76
votes
2
replies
50k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
tutorial
Tutorial
written 9.0 years ago by
Eric Normandeau
11k
12
votes
5
replies
9.6k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
gene
RNA-Seq
R
Tutorial
updated 7 weeks ago by
Kevin Blighe
81k • written 4.6 years ago by
ahmad mousavi
▴ 640
1
vote
0
replies
435
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA
Counts
v32.0
Biolinks
GDC
STAR
10 weeks ago by
dare_devil
★ 1.6k
29
votes
3
replies
6.5k
views
7 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
Tutorial
cancer
methylation
R
updated 11 weeks ago by
GenoMax
117k • written 21 months ago by
Hamid Ghaedi
★ 2.5k
1
vote
2
replies
473
views
Tutorial:
Running fastq_screen on your data
fastqscreen
3 months ago by
rohitsatyam102
▴ 510
7
votes
12
replies
979
views
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 4 months ago by
Shred
▴ 640 • written 4 months ago by
thehung92phuyen
▴ 30
70
votes
14
replies
12k
views
15 follow
Tutorial:
List Of Bioinformatics Books
bioinformatics
tutorial
books
Tutorial
updated 4 months ago by
Paul A. Gagniuc
▴ 30 • written 9.1 years ago by
Medhat
9.3k
23
votes
13
replies
2.8k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 5 months ago by
liorglic
▴ 880 • written 8 months ago by
Istvan Albert
93k
3
votes
13
replies
6.7k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
merge
bcftools
Tutorial
written 3.4 years ago by
jaybee
▴ 140
12
votes
9
replies
1.9k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 14 days ago by
dk0319
▴ 30 • written 6 months ago by
Barry Digby
▴ 980
9
votes
0
replies
824
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
5 months ago by
dariober
13k
2
votes
0
replies
599
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell
Biology
R
Computational
signalling
5 months ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
2.7k
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
5 months ago by
Wayne
★ 1.2k
12
votes
4
replies
3.6k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial
linux
bioinformatics
R
updated 7 months ago by
iamsmor
• 0 • written 16 months ago by
garden_giessen
▴ 120
21
votes
10
replies
37k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
Tutorial
error
software
R
updated 4 weeks ago by
Chih
• 0 • written 15 months ago by
Nitin Narwade
★ 1.2k
1
vote
0
replies
1.1k
views
Tutorial:
Unsupervised clustering on gene expression data
clustering
RNA-seq
expression
gene
3 months ago by
Hamid Ghaedi
★ 2.5k
35
votes
6
replies
12k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 5 months ago by
cameron.cowan
▴ 10 • written 15 months ago by
rpolicastro
8.8k
139
votes
67
replies
38k
views
17 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
updated 8 months ago by
Hamtaro
▴ 10 • written 4.6 years ago by
Kevin Blighe
81k
122
votes
119
replies
23k
views
22 follow
Tutorial:
Survival analysis with gene expression
survival analysis
cox
geo
gene expression
Tutorial
6 weeks ago by
Kevin Blighe
81k
14
votes
1
reply
944
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 9 months ago by
dariober
13k • written 9 months ago by
nhaus
▴ 200
192
votes
47
replies
66k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
tutorial
bioconductor
microarray
analysis
tutorial
Tutorial
updated 4 months ago by
javanokendo
▴ 10 • written 9.7 years ago by
Obi Griffith
19k
20
votes
1
reply
1.7k
views
Tutorial:
Building Docker images
singularity
container
docker
9 months ago by
ATpoint
62k
6
votes
2
replies
718
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
10 months ago by
Kevin Blighe
81k
0
votes
0
replies
646
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
10 months ago by
mo
• 0
1
vote
0
replies
853
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
10 months ago by
Kevin Blighe
81k
45
votes
2
replies
34k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
tutorial
Tutorial
updated 11 months ago by
kjh98
• 0 • written 10.2 years ago by
MSU course 2011
▴ 540
86
votes
95
replies
28k
views
23 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 6 weeks ago by
dongxinyu510
• 0 • written 3.8 years ago by
Kevin Blighe
81k
70
votes
19
replies
9.3k
views
15 follow
Tutorial:
Gene Set Enrichment Analysis
enrichment
microarray
Tutorial
GSEA
RNA-Seq
8 weeks ago by
Hamid Ghaedi
★ 2.5k
0
votes
0
replies
514
views
Tutorial:
Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation
bioimaging
SLURM
health
12 months ago by
Erin Haskell | ELIXIR
▴ 460
1
vote
0
replies
701
views
Tutorial:
Slurm and parallelization
slurm
12 months ago by
Juke34
★ 7.1k
1
vote
0
replies
615
views
Tutorial:
How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo
cytoscape
12 months ago by
Pratik
▴ 770
12
votes
1
reply
1.3k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 12 months ago by
jared.andrews07
★ 13k • written 12 months ago by
Kevin Blighe
81k
113
votes
66
replies
35k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
ENA
Fastq
Tutorial
11 months ago by
ATpoint
62k
4
votes
0
replies
641
views
Tutorial:
Long Read Genome Assembly Video Series
long-read
genome-assembly
12 months ago by
pbpanigrahi
▴ 410
0
votes
1
reply
504
views
Tutorial:
Add Customized Filters in GDC
gdc
updated 13 months ago by
cpad0112
20k • written 13 months ago by
Zhenyu Zhang
▴ 540
61
votes
26
replies
8.4k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
bam
consensus
fasta
Tutorial
updated 13 months ago by
bioinfo8
▴ 180 • written 3.3 years ago by
finswimmer
15k
11
votes
20
replies
9.5k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat
single cell
RNA-Seq
TCR
Tutorial
13 months ago by
jared.andrews07
★ 13k
4
votes
2
replies
1.6k
views
Tutorial:
Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0
Tutorial
updated 13 months ago by
GenoMax
117k • written 3.0 years ago by
Shicheng Guo
★ 9.1k
32
votes
13
replies
30k
views
9 follow
Tutorial:
Using R in Conda
R
Tutorial
updated 3 months ago by
Siddharth
• 0 • written 23 months ago by
rohitsatyam102
▴ 510
31
votes
9
replies
16k
views
11 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
Tutorial
updated 4 weeks ago by
Verónica
• 0 • written 22 months ago by
lavinia.gordon
▴ 140
98
votes
16
replies
27k
views
18 follow
Tutorial:
Heatmaps in R
Tutorial
R
heatmap
7 weeks ago by
Jean-Karim Heriche
25k
18
votes
1
reply
2.1k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 14 months ago by
Michael Dondrup
51k • written 14 months ago by
Juke34
★ 7.1k
31
votes
6
replies
6.3k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
complexheatmap
clustering
arthritis
pam
Tutorial
10 months ago by
Kevin Blighe
81k
75
votes
40
replies
25k
views
23 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 3 months ago by
Ram
36k • written 8.7 years ago by
Irsan
★ 7.5k
8
votes
0
replies
1.5k
views
Tutorial:
Pipes in R: An introduction and some advanced tips and tricks.
R
15 months ago by
rpolicastro
8.8k
233
votes
176
replies
78k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 3 months ago by
Ram
36k • written 6.9 years ago by
TriS
★ 4.5k
6
votes
0
replies
945
views
Tutorial:
data.frames in R: How vectorization can save you time and heartache
R
15 months ago by
rpolicastro
8.8k
8
votes
1
reply
742
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk
fasta
Tutorial
15 months ago by
Kevin Blighe
81k
15
votes
9
replies
3.2k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R
tidyverse
gene
Tutorial
updated 9 months ago by
krushnach80
★ 1.1k • written 22 months ago by
rpolicastro
8.8k
12
votes
2
replies
816
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
Tutorial
15 months ago by
rpolicastro
8.8k
348 results • Page
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Recent Votes
Answer: ESTIMATE tumor purity
C: Run PHI-BLAST in BLAST+ standalone
Answer: Junior bioinformatician in italy
Junior bioinformatician in italy
A: Thoughts on switching from Biology to Bioinformatics
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Replies
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
If 1kgtot.bim contains doubled IDs (e.g. "HG00096 HG00096", you need to provide a doubled ID to `--indv`. The log file shows that your scr…
Answer: ESTIMATE tumor purity
by
JACKY
▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST
by
GenoMax
117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage
by
Neel
▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST
by
Pilar
• 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput
by
Ying
• 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
by
Mensur Dlakic
★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
kalavattam
▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★ 13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
Answer: Get nucleotide sequence of assembled RNA transcripts
by
tomas4482
▴ 140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
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