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108 results • Page
1 of 3
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Votes
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276
votes
39
replies
165k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 7 days ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
144
votes
69
replies
43k
views
19 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 1 day ago by
k001
▴ 10 • written 5.4 years ago by
Kevin Blighe
85k
130
votes
123
replies
29k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 10 days ago by
krushnach80
★ 1.1k • written 4.5 years ago by
Kevin Blighe
85k
116
votes
66
replies
40k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 18 days ago by
Ram
38k • written 4.7 years ago by
ATpoint
71k
100
votes
6
replies
22k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 17 days ago by
Ram
38k • written 4.6 years ago by
finswimmer
16k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 17 days ago by
Ram
38k • written 6.7 years ago by
Jean-Karim Heriche
26k
92
votes
105
replies
34k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 18 days ago by
Ram
38k • written 4.6 years ago by
Kevin Blighe
85k
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork
enrichment
pathway
R
updated 22 days ago by
Ram
38k • written 4.8 years ago by
egeulgen
★ 1.3k
82
votes
21
replies
15k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 22 days ago by
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
2.9k
81
votes
8
replies
7.8k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 25 days ago by
Ram
38k • written 8.8 years ago by
Malachi Griffith
19k
75
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 17 days ago by
Ram
38k • written 5.1 years ago by
Kevin Blighe
85k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 29 days ago by
Ram
38k • written 9.1 years ago by
Istvan Albert
97k
64
votes
26
replies
11k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 18 days ago by
Ram
38k • written 4.1 years ago by
finswimmer
16k
64
votes
26
replies
11k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 17 days ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
85k
60
votes
52
replies
39k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 17 days ago by
Ram
38k • written 6.5 years ago by
steve
★ 3.3k
59
votes
43
replies
18k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 17 days ago by
Ram
38k • written 5.5 years ago by
Rox
★ 1.4k
58
votes
25
replies
36k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 14 days ago by
Ram
38k • written 6.7 years ago by
Shicheng Guo
★ 9.3k
50
votes
3
replies
4.0k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 17 days ago by
Ram
38k • written 4.2 years ago by
ATpoint
71k
45
votes
14
replies
59k
views
10 follow
Tutorial:
Using R in Conda
R
updated 17 days ago by
Ram
38k • written 2.7 years ago by
rohitsatyam102
▴ 690
43
votes
6
replies
11k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 29 days ago by
Ram
38k • written 9.2 years ago by
Cyriac Kandoth
5.9k
42
votes
33
replies
6.8k
views
8 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta
how-to
documentation
17 days ago by
Ram
38k
40
votes
9
replies
10k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 25 days ago by
Ram
38k • written 9.0 years ago by
Ahill
★ 1.9k
37
votes
8
replies
9.3k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
R
methylation
updated 22 days ago by
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
2.9k
34
votes
15
replies
5.1k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 17 days ago by
Ram
38k • written 3.8 years ago by
Shicheng Guo
★ 9.3k
34
votes
15
replies
18k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 16 days ago by
Ram
38k • written 6.5 years ago by
martinguerrerog89
▴ 310
32
votes
4
replies
6.4k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 14 days ago by
Ram
38k • written 4.4 years ago by
firestar
★ 1.5k
31
votes
9
replies
24k
views
11 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 17 days ago by
Ram
38k • written 2.6 years ago by
lavinia.gordon
▴ 140
31
votes
6
replies
8.7k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 17 days ago by
Ram
38k • written 2.9 years ago by
Kevin Blighe
85k
30
votes
8
replies
10k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 25 days ago by
Ram
38k • written 9.0 years ago by
Rad
▴ 800
28
votes
4
replies
3.7k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 16 days ago by
Ram
38k • written 4.2 years ago by
Jean-Karim Heriche
26k
26
votes
0
replies
2.1k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 17 days ago by
Ram
38k • written 3.5 years ago by
Malachi Griffith
19k
26
votes
10
replies
59k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 22 days ago by
Ram
38k • written 2.0 years ago by
Nitin Narwade
★ 1.3k
23
votes
4
replies
6.2k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 17 days ago by
Ram
38k • written 3.6 years ago by
ATpoint
71k
20
votes
4
replies
2.2k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 17 days ago by
Ram
38k • written 3.9 years ago by
nim.1111.ou
▴ 180
20
votes
10
replies
4.7k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 17 days ago by
Ram
38k • written 2.6 years ago by
rpolicastro
11k
20
votes
7
replies
5.6k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 17 days ago by
Ram
38k • written 4.5 years ago by
ahmad mousavi
▴ 740
20
votes
6
replies
4.8k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 17 days ago by
Ram
38k • written 6.5 years ago by
Denise CS
★ 5.2k
18
votes
22
replies
7.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 17 days ago by
Ram
38k • written 3.3 years ago by
Juke34
7.8k
18
votes
40
replies
16k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 17 days ago by
Ram
38k • written 6.8 years ago by
Esaie
▴ 170
16
votes
11
replies
13k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 17 days ago by
Ram
38k • written 6.4 years ago by
TriS
★ 4.6k
16
votes
11
replies
7.3k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
17 days ago by
Ram
38k
16
votes
7
replies
12k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 17 days ago by
Ram
38k • written 3.8 years ago by
atakanekiz
▴ 310
15
votes
2
replies
2.7k
views
Tutorial:
Introduction to bedtools.
bedtools
updated 22 days ago by
Ram
38k • written 8.4 years ago by
Aaronquinlan
11k
15
votes
5
replies
11k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 22 days ago by
Ram
38k • written 5.3 years ago by
ahmad mousavi
▴ 740
15
votes
4
replies
4.1k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 17 days ago by
Ram
38k • written 2.7 years ago by
Thind amarinder
▴ 300
14
votes
7
replies
5.5k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 17 days ago by
Ram
38k • written 6.9 years ago by
steve
★ 3.3k
14
votes
2
replies
6.1k
views
Tutorial:
ChIP-seq analysis tutorial
ChIP-Seq
updated 1 day ago by
Ram
38k • written 7.6 years ago by
Ming Tommy Tang
★ 2.9k
14
votes
2
replies
2.8k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 17 days ago by
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
2.9k
12
votes
4
replies
1.8k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 8 days ago by
Ram
38k • written 5.6 years ago by
KVC_bioinfo
▴ 570
12
votes
20
replies
11k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 17 days ago by
Ram
38k • written 3.8 years ago by
jared.andrews07
★ 14k
108 results • Page
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Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Comment: pyCirclize - Circular visualization in Python
by
moshi
▴ 90
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data
by
Dion
• 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R
by
Eliza
▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
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