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806 results • Page
1 of 17
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1
vote
1
reply
19
views
Saving results from yeastgenome.org blastp search
blast
blastp
updated 10 minutes ago by
GenoMax
130k • written 1 hour ago by
dec986
▴ 360
1
vote
1
reply
27
views
Differences in GTF files hg19 and hg38
hg38
hg19
GTF
updated 43 minutes ago by
Ram
39k • written 1 hour ago by
heureuse
• 0
0
votes
0
replies
24
views
normalize for sample size in single cell rna seq cluster frequencies data
scRNAseq
seurat
10x
3 hours ago by
chi.delta
▴ 40
1
vote
3
replies
111
views
counts matrix should be numeric, currently it has mode: character when using a csv file in R for DESeq2
DESeq2
updated 50 minutes ago by
Ram
39k • written 3 hours ago by
Sara
▴ 220
0
votes
1
reply
46
views
sgRNA design
gene-editing
updated 2 hours ago by
Ram
39k • written 3 hours ago by
elisa.qinxue
• 0
1
vote
1
reply
41
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 3 hours ago by
GenoMax
130k • written 3 hours ago by
saint-even
• 0
0
votes
0
replies
29
views
TCGA input files for COHCAP
TCGA
methylation
COHCAP
4 hours ago by
dilrajkaur766
• 0
0
votes
0
replies
33
views
m6A-seq input normalisation with RNA-seq
m6A-seq
MeRIP-Seq
normalisation
deepTools
updated 4 hours ago by
Ram
39k • written 4 hours ago by
Pari
• 0
0
votes
1
reply
63
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
updated 47 minutes ago by
Ram
39k • written 4 hours ago by
aaronlogsdon2001
• 0
16
votes
8
replies
254
views
Tool:
ChatGPT optimized for bioinformatics questions
gpt
1 hour ago by
Sasha
▴ 280
2
votes
4
replies
274
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 10 minutes ago by
Rory Stark
★ 1.8k • written 2 days ago by
B.N.
• 0
2
votes
3
replies
218
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
1 hour ago by
B.N.
• 0
0
votes
0
replies
30
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
5 hours ago by
cate.cevallos
• 0
1
vote
4
replies
135
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
updated 3 hours ago by
ATpoint
72k • written 5 hours ago by
Zhichao
• 0
0
votes
1
reply
60
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 5 hours ago by
ATpoint
72k • written 6 hours ago by
f2ff7a46
• 0
0
votes
1
reply
71
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 5 hours ago by
ATpoint
72k • written 6 hours ago by
t.ru
▴ 20
0
votes
1
reply
57
views
Visualizing several genomes/plasmids in a single figure
visualization
updated 5 hours ago by
GenoMax
130k • written 6 hours ago by
blur
▴ 270
1
vote
1
reply
67
views
switching from illumination to NEB prep kits
NEB
WGS
WES
illumina
updated 5 hours ago by
GenoMax
130k • written 6 hours ago by
lait
▴ 170
4
votes
13
replies
472
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
updated 5 hours ago by
ATpoint
72k • written 1 day ago by
melissachua90
▴ 40
4
votes
8
replies
238
views
Extract sequences from a fastq file by a list of IDs
fastq
updated 30 minutes ago by
Ram
39k • written 11 hours ago by
mhpakdel96
▴ 10
0
votes
0
replies
30
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
6 hours ago by
Sapphire
• 0
0
votes
0
replies
45
views
Complex Phylogenetic Tree Annotation
annotation
protein
phylogenetic-tree
updated 4 hours ago by
Ram
39k • written 7 hours ago by
Aanushka
• 0
0
votes
2
replies
1.6k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 8 hours ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
0
votes
0
replies
42
views
impute tool /imputing GTs _ generated imputed file has unexpected no. of cols
haplotype
impute
imputing
snps
ref
8 hours ago by
SalmaElShafie
• 0
1
vote
3
replies
125
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 6 hours ago by
Darked89
4.4k • written 8 hours ago by
Ayish
• 0
0
votes
3
replies
95
views
Is PanCan data microarray or rna-seq
pancan
rna
rna-seq
microarray
data
updated 1 hour ago by
GenoMax
130k • written 11 hours ago by
survive
• 0
0
votes
1
reply
81
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 12 hours ago by
seidel
11k • written 12 hours ago by
dare_devil
★ 3.1k
0
votes
1
reply
155
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
13 hours ago by
Apprentice
▴ 140
6
votes
8
replies
630
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
12 hours ago by
Chris
▴ 100
0
votes
2
replies
2.8k
views
How to run Picard docker image
next-gen
alignment
docker
picard
updated 18 hours ago by
geocarvalho
▴ 330 • written 3.7 years ago by
elcortegano
▴ 180
0
votes
0
replies
84
views
Job:
Associate Professor, Ecology
Ecology
updated 19 hours ago by
Ram
39k • written 19 hours ago by
jterakita
▴ 20
0
votes
2
replies
151
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
8 hours ago by
JACKY
▴ 100
0
votes
1
reply
113
views
CIBERSORT Error: File not found
CIBERSORT
updated 10 hours ago by
ATpoint
72k • written 20 hours ago by
jcara514
• 0
3
votes
4
replies
221
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 4 hours ago by
Ram
39k • written 22 hours ago by
shamza
• 0
0
votes
3
replies
228
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 19 hours ago by
Ram
39k • written 1 day ago by
Researcher
• 0
7
votes
6
replies
319
views
Contigs to chromosomes annotation
Assembly
mapping
contigs
updated 23 hours ago by
GenoMax
130k • written 1 day ago by
alexandru.bologa.marian
▴ 50
3
votes
4
replies
273
views
Gene prediction software
pseudogene
gene
prediction
masking
updated 9 hours ago by
Darked89
4.4k • written 1 day ago by
subashini.fbtpb106
▴ 20
1
vote
0
replies
104
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
1 day ago by
zhangdengwei
▴ 190
1
vote
2
replies
169
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
4 hours ago by
tahsinkhan570
• 0
2
votes
3
replies
221
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 1 day ago by
GenoMax
130k • written 1 day ago by
ev97
• 0
0
votes
0
replies
113
views
Which is the minor allele in ped file in plink?
plink
updated 1 day ago by
GenoMax
130k • written 1 day ago by
khn
▴ 130
0
votes
2
replies
194
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
20 hours ago by
mattze731
▴ 10
1
vote
1
reply
252
views
Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
16S
dada2
DECIPHER
ITS
taxonomy
1 day ago by
mattze731
▴ 10
0
votes
0
replies
108
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
1 day ago by
F.Bedjou
▴ 10
0
votes
0
replies
108
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
1 day ago by
Coremine Medical
▴ 10
2
votes
1
reply
169
views
Visualizing Graph Alignment Format via minigraph
graph
gaf
minigraph
alignment
updated 1 day ago by
colindaven
4.9k • written 1 day ago by
ivazirabad
▴ 20
0
votes
2
replies
239
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 1 day ago by
ATpoint
72k • written 5 days ago by
fr
▴ 200
1
vote
2
replies
257
views
What kind of statistical test does Cellranger count use?
scRNAseq
10X
Single-Cell
updated 1 day ago by
fracarb8
▴ 950 • written 1 day ago by
hannah
• 0
3
votes
7
replies
4.2k
views
Getting Pairwise Sequence Alignment Score With Biopython
biopython
alignment
clustalw
updated 1 day ago by
Jonathan Lefebre
▴ 70 • written 11.5 years ago by
Lakshmi
• 0
0
votes
0
replies
92
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
1 day ago by
hashim.rana11
▴ 20
806 results • Page
1 of 17
Recent Votes
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Comment: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
Answer: CHiP-Seq Questions
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Recent Awards •
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GenoMax
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Recent Replies
Comment: Saving results from yeastgenome.org blastp search
by
GenoMax
130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions
by
B.N.
• 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions
by
B.N.
• 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq
by
GenoMax
130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq
by
solarchan7
• 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome
by
Basti
★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions
by
ATpoint
72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design
by
ATpoint
72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
ATpoint
72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing
by
GenoMax
130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
Comment: Is there bioinformatics tool to check cross hybridization between primers and pr
by
Tawny
▴ 180
Was a tool ever found for this? I am curious.
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