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1,000 results • Page
4 of 20
Sort: Views
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Views
Votes
Replies
6
votes
7
replies
48k
views
matching and merging data frames of different lengths
R
updated 17 months ago by
Ram
38k • written 8.8 years ago by
Diana
▴ 900
24
votes
7
replies
48k
views
What Databases Are Available For Rna-Seq Datasets?
rna-seq
database
geo
updated 10.8 years ago by
Khader Shameer
18k • written 10.8 years ago by
aprathke
▴ 140
38
votes
41
replies
48k
views
9 follow
Volcano Plot from DEseq2
R
written 5.4 years ago by
krushnach80
★ 1.1k
30
votes
20
replies
48k
views
11 follow
List Of All Transcription Factors In Human
transcription
ensembl
genes
updated 10.5 years ago by
Alex Reynolds
34k • written 10.5 years ago by
dfernan
▴ 720
60
votes
15
replies
48k
views
11 follow
Estimate Insert Size In Paired-End/Mate-Pair
next-gen
sequencing
alignment
paired
updated 17 months ago by
Ram
38k • written 11.2 years ago by
Ric
▴ 190
1.2k
votes
205
replies
48k
views
107 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 weeks ago by
jena
▴ 250 • written 12.0 years ago by
Jeremy Leipzig
21k
44
votes
10
replies
48k
views
7 follow
RNA-seq: Explain STAR quantMode geneCounts values
RNA-Seq
STAR
Differential expression
updated 5.0 years ago by
Tao
▴ 490 • written 6.4 years ago by
williantafsilva
▴ 330
89
votes
21
replies
48k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq
read
updated 9.3 years ago by
earonesty
▴ 240 • written 10.4 years ago by
siddharth.sethi5
▴ 270
87
votes
37
replies
48k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 12 months ago by
Ram
38k • written 9.7 years ago by
Hunter
▴ 110
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R
ggplot
plots
colors
updated 6.5 years ago by
Biostar
20 • written 6.7 years ago by
james.lloyd
▴ 100
45
votes
3
replies
48k
views
Gwas Vs. Qtl Mapping?
gwas
mapping
updated 9 months ago by
Ram
38k • written 10.8 years ago by
Justin
▴ 460
50
votes
33
replies
48k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq
DEseq2
R
updated 4.9 years ago by
Kevin Blighe
85k • written 6.7 years ago by
ta_awwad
▴ 320
36
votes
8
replies
48k
views
10 follow
Adding Read Groups To Bam Files
bam
gatk
samtools
bwa
updated 21 months ago by
zx8754
11k • written 10.8 years ago by
Zev.Kronenberg
12k
10
votes
4
replies
48k
views
BLAST: Identity % and Similarity %
blast
updated 6.8 years ago by
natasha.sernova
★ 3.9k • written 6.8 years ago by
hnp21
▴ 40
97
votes
12
replies
47k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl
entrez
gene
updated 2.0 years ago by
hagenaue
▴ 10 • written 11.2 years ago by
Untom
▴ 420
0
votes
3
replies
47k
views
Tutorial:
Installation VMD on LINUX_64
VMD
VMD installation
gromacs
Tutorial
updated 6.8 years ago by
Michael D
52k • written 6.8 years ago by
Hassan Rasouli
▴ 10
65
votes
9
replies
47k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 7 weeks ago by
Ram
38k • written 9.8 years ago by
Joseph Hughes
★ 3.0k
22
votes
4
replies
47k
views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools
plink
ped
map
updated 4.1 years ago by
hakimeazarafra
• 0 • written 8.5 years ago by
roll
▴ 350
0
votes
6
replies
47k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R
heatmap
error
updated 22 months ago by
Abdul Aziz
• 0 • written 4.0 years ago by
luzglongoria
▴ 40
45
votes
11
replies
47k
views
10 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 8 months ago by
Ram
38k • written 7.2 years ago by
nash.claire
▴ 470
57
votes
15
replies
46k
views
11 follow
Filtering Vcf File
vcftools
vcf
snp
indel
updated 13 months ago by
Ram
38k • written 10.6 years ago by
bioinfo
▴ 830
29
votes
9
replies
46k
views
What Is The Difference Between Sequencing Depth And Coverage
sequencing
read
coverage
updated 12.0 years ago by
Michael D
52k • written 12.0 years ago by
User 6659
▴ 970
66
votes
18
replies
46k
views
16 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
tools
updated 18 days ago by
Muhammad
• 0 • written 10.1 years ago by
14134125465346445
★ 3.6k
11
votes
13
replies
45k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R
RNA-Seq
pheatmap
arg10
updated 2.2 years ago by
henry-keen
▴ 40 • written 2.8 years ago by
camillab.
▴ 130
13
votes
5
replies
45k
views
7 follow
Obtaining The Snp Rs Number With The Chromosomal Position
r
snps
bioconductor
updated 18 months ago by
krassowski.michal
▴ 170 • written 9.9 years ago by
Sheila
▴ 410
88
votes
52
replies
45k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 16 months ago by
BioNovice247
▴ 10 • written 5.4 years ago by
rachel.kubik12
▴ 210
29
votes
10
replies
45k
views
How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
fastq
paired-end
illumina
updated 9.0 years ago by
Chris Fields
★ 2.2k • written 9.1 years ago by
fbrundu
▴ 330
51
votes
21
replies
45k
views
11 follow
Fastq Splitter For Paired End Reads
rna
paired
tool
updated 15 months ago by
Ram
38k • written 11.0 years ago by
Geparada
★ 1.5k
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 7 months ago by
Ram
38k • written 11.9 years ago by
Matthieu
▴ 480
34
votes
5
replies
44k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap
R
updated 7 weeks ago by
Ram
38k • written 6.1 years ago by
emil.bb
▴ 170
35
votes
6
replies
44k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen
RNA-Seq
single-cell
R
updated 22 months ago by
jared.andrews07
★ 14k • written 3.3 years ago by
Payal
▴ 140
54
votes
52
replies
44k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Tool
on
Gene
Clustering
Function
based
updated 15 months ago by
Ram
38k • written 8.7 years ago by
EagleEye
7.4k
32
votes
19
replies
44k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
convert
updated 3 months ago by
Ram
38k • written 9.8 years ago by
hicsuntdrac0nis
▴ 240
5
votes
3
replies
44k
views
Extract the values by matching two rows of one dataframe with the two columns of another dataframe
dataframe
match
updated 10 months ago by
Ram
38k • written 8.1 years ago by
MAPK
★ 2.0k
2
votes
3
replies
44k
views
Convert text file to VCF file ?
vcf
updated 3.9 years ago by
zx8754
11k • written 8.1 years ago by
CrazyB
▴ 260
31
votes
5
replies
43k
views
What is Differential Expression?
DNA
genes
updated 15 months ago by
Ram
38k • written 8.6 years ago by
LoveLeh
▴ 40
39
votes
16
replies
43k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen
sra
fastq
updated 13 months ago by
Alejandro Miguel
▴ 10 • written 6.4 years ago by
thustar
▴ 120
17
votes
3
replies
43k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr
sequencing
updated 9.7 years ago by
William
★ 5.2k • written 9.7 years ago by
weiqiangduan
▴ 130
77
votes
18
replies
43k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 8 months ago by
Dan
• 0 • written 12.9 years ago by
Science_Robot
★ 1.1k
48
votes
4
replies
43k
views
How To Convert The Bed File To Ped File
bed
ped
updated 6 months ago by
sonsunjirachote
• 0 • written 12.6 years ago by
Austinlew
▴ 310
6
votes
12
replies
43k
views
9 follow
Opening A Fasta File In Windows
fasta
blast
makeblastdb
updated 11.1 years ago by
Vivek
• 0 • written 11.1 years ago by
Vivek
• 0
29
votes
10
replies
43k
views
Filtering A Sam File For Quality Scores
sam
updated 10.9 years ago by
Sukhi Singh
11k • written 10.9 years ago by
Varun Gupta
★ 1.2k
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
124
votes
46
replies
43k
views
20 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq
visualization
deeptools
ngsplot
homer
Forum
updated 20 months ago by
Chirag Nepal
★ 2.3k • written 7.1 years ago by
Sinji
★ 3.2k
21
votes
5
replies
43k
views
Any Method Of Converting Bigwig File Format Into Bed Format?
bigwig
bed
updated 3.8 years ago by
Samir
▴ 190 • written 9.9 years ago by
samwise.techno
▴ 50
63
votes
8
replies
43k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq
cdna
updated 6.6 years ago by
SeqFreak
• 0 • written 10.5 years ago by
Justin
▴ 460
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 8 weeks ago by
Ram
38k • written 7.9 years ago by
MAPK
★ 2.0k
13
votes
14
replies
43k
views
7 follow
Convert SAM to BAM
sam
RNA-Seq
bam
updated 15 months ago by
Ram
38k • written 8.7 years ago by
marina-orlova
▴ 80
21
votes
11
replies
42k
views
reading a bed file in R
bed
R
updated 16 months ago by
Ram
38k • written 7.3 years ago by
fi1d18
★ 4.1k
31
votes
7
replies
42k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq
deseq2
tpm
updated 8 months ago by
Ram
38k • written 8.1 years ago by
Tom Harrop
▴ 170
1,000 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: 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…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
by
Daniel
• 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
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