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412 results • Page
3 of 9
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Votes
Replies
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 13 months ago by
Ram
43k • written 7.7 years ago by
zizigolu
★ 4.3k
20
votes
4
replies
2.7k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 14 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
20
votes
0
replies
8.8k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
19
votes
3
replies
14k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 22 months ago by
Ram
43k • written 8.3 years ago by
Shicheng Guo
★ 9.4k
19
votes
7
replies
6.7k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 10 months ago by
ATpoint
82k • written 4.1 years ago by
colindaven
6.4k
19
votes
4
replies
8.9k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 15 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
18
votes
2
replies
10k
views
Tutorial:
Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq
Galaxy
IGB
updated 2.2 years ago by
Ram
43k • written 9.6 years ago by
Nowlan Freese
▴ 860
18
votes
40
replies
18k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.9 years ago by
krishdb38
• 0 • written 7.9 years ago by
Esaie
▴ 170
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 12 months ago by
Ram
43k • written 7.0 years ago by
Sej Modha
5.3k
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 12 months ago by
Ram
43k • written 7.1 years ago by
Michael
54k
17
votes
0
replies
6.6k
views
Tutorial:
Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course
training
updated 15 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
17
votes
0
replies
13k
views
Tutorial:
Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 15 months ago by
Ram
43k • written 12.1 years ago by
David Langenberger
11k
16
votes
6
replies
6.5k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Botond Sipos
★ 1.7k
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
16
votes
5
replies
9.0k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Obi Griffith
20k
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
16
votes
11
replies
8.3k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
14 months ago by
Ram
43k
16
votes
9
replies
7.2k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 23 months ago by
dk0319
▴ 70 • written 2.5 years ago by
Barry Digby
★ 1.3k
16
votes
11
replies
14k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 14 months ago by
Ram
43k • written 7.6 years ago by
TriS
★ 4.7k
16
votes
3
replies
4.7k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
updated 13 months ago by
Ram
43k • written 8.1 years ago by
Eric Normandeau
11k
16
votes
3
replies
4.4k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 3.2 years ago by
zhuanggj706
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
15
votes
4
replies
4.6k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
Thind amarinder
▴ 340
15
votes
2
replies
6.9k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
15
votes
7
replies
6.5k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 14 months ago by
Ram
43k • written 8.0 years ago by
steve
★ 3.5k
15
votes
2
replies
3.1k
views
Tutorial:
Introduction to bedtools.
bedtools
updated 14 months ago by
Ram
43k • written 9.5 years ago by
Aaronquinlan
12k
15
votes
5
replies
16k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Obi Griffith
20k
15
votes
1
reply
4.0k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 20 months ago by
Assa Yeroslaviz
★ 1.8k • written 2.4 years ago by
dariober
14k
15
votes
1
reply
3.2k
views
Tutorial:
Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics
training
lectures
workshop
updated 13 months ago by
Ram
43k • written 8.0 years ago by
Malachi Griffith
20k
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
15
votes
1
reply
7.2k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Joseph Hughes
★ 3.0k
14
votes
0
replies
9.6k
views
Tutorial:
How to generate PCA plot and heatmaps in R
heatmap
PCA
RNA-Seq
R
updated 13 months ago by
Ram
43k • written 7.7 years ago by
Ming Tommy Tang
★ 3.9k
14
votes
3
replies
20k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 9 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
14
votes
1
reply
3.1k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 3.0 years ago by
jared.andrews07
★ 16k • written 3.0 years ago by
Kevin Blighe
88k
14
votes
0
replies
8.4k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Nowlan Freese
▴ 860
14
votes
31
replies
6.9k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 14 months ago by
Ram
43k • written 4.8 years ago by
Juke34
8.6k
14
votes
2
replies
6.5k
views
Tutorial:
ChIP-seq analysis tutorial
ChIP-Seq
updated 13 months ago by
Ram
43k • written 8.7 years ago by
Ming Tommy Tang
★ 3.9k
14
votes
2
replies
2.4k
views
Tutorial:
Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP
R
updated 13 months ago by
Ram
43k • written 8.2 years ago by
Jeremy Leipzig
22k
13
votes
6
replies
6.0k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 13 months ago by
Ram
43k • written 7.9 years ago by
dariober
14k
13
votes
7
replies
6.3k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
Chromium
10x
STARsolo
STAR
updated 14 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
13
votes
3
replies
5.2k
views
Tutorial:
Video: Visualization of whole genome DNA methylation data in IGB
Bismark
BS-Seq
RNA-Seq
IGB
updated 24 months ago by
Ram
43k • written 9.2 years ago by
Nowlan Freese
▴ 860
12
votes
5
replies
8.4k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by
Ram
43k • written 8.0 years ago by
Shicheng Guo
★ 9.4k
12
votes
4
replies
2.2k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 14 months ago by
Ram
43k • written 6.7 years ago by
KVC_bioinfo
▴ 590
12
votes
0
replies
2.8k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
ggplot2
tidyverse
data.table
R
updated 14 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
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
12
votes
6
replies
5.0k
views
Tutorial:
sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 22 months ago by
Ram
43k • written 8.3 years ago by
zizigolu
★ 4.3k
12
votes
5
replies
2.5k
views
Tutorial:
FASTA file split
fasta
updated 14 months ago by
Ram
43k • written 3.9 years ago by
Juke34
8.6k
12
votes
0
replies
7.9k
views
Tutorial:
Plot average methylation levels across TSS region
bedtools
RRBS
R
methylation
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
TriS
★ 4.7k
12
votes
7
replies
2.3k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
13 months ago by
barslmn
★ 2.2k
12
votes
1
reply
5.1k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 19 months ago by
Ram
43k • written 8.8 years ago by
mikhail.shugay
3.5k
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 5.0 years ago by
jared.andrews07
★ 16k
412 results • Page
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Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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carlopecoraro2
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▴ 30
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Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
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scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
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