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Showing top results for tag:
target
•
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0
votes
1
reply
276
views
RNAhybrid + svm_light for miRNA target prediction
microrna
svm
target
rnahybrid
updated 3 days ago by
bingyanzheng18
• 0 • written 3 months ago by
Lucrezia
• 0
0
votes
0
replies
144
views
Long non-coding RNA target
target
gene
lncRNA
6 days ago by
zizigolu
★ 4.3k
0
votes
1
reply
251
views
How to Predict Drug Targets Using Single-Sample RNA-Seq Data?
Drug
Target
RNA-Seq
updated 4 months ago by
DGTool
▴ 290 • written 4 months ago by
Musab
• 0
13
votes
3
replies
657
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 5 months ago by
b.contreras.moreira
▴ 300 • written 5 months ago by
ijarne
▴ 10
0
votes
1
reply
451
views
How to find clinical data for TARGET AML
TARGET
AML
updated 8 months ago by
Zhenyu Zhang
★ 1.2k • written 8 months ago by
veronique.voisin
• 0
1
vote
2
replies
890
views
Is it possible to find the target bed file for TSO500 panel?
bed
illumina
target
updated 12 months ago by
a.loka92
• 0 • written 13 months ago by
Danchurova
• 0
1
vote
1
reply
425
views
Cancer drug target identification from gene expression data of patients?
cancer
gene
target
updated 12 months ago by
Matthias Zepper
4.9k • written 12 months ago by
Benedek Dankó
▴ 50
0
votes
1
reply
609
views
Are there any recommended tools for tumor target sequencing data downstream analysis
target
tumor
downstream
compare
plots
17 months ago by
alwayshope
▴ 40
1
vote
3
replies
944
views
Extracting list of target genes from ChIP-seq bigwig file
target
ChIP-seq
bigwig
gene
updated 21 months ago by
ATpoint
85k • written 21 months ago by
jennifer.conrad84
▴ 10
3
votes
2
replies
851
views
Question regarding miRNA target gene prediction
target
prediction
miRNA
gene
22 months ago by
kuttibiotech2009
▴ 30
3
votes
9
replies
2.4k
views
CNVKit does not output all the accessible regions in the targets bed file
CNVkit
cnv
bed
target
wgs
23 months ago by
ashenflower
▴ 30
0
votes
0
replies
497
views
Sylamer analysis for detecting microRNA binding
sylamer
differential
microRNAs
RNA-seq
identification
expression
target
analysis
gene
24 months ago by
faiza.altaf
• 0
0
votes
1
reply
615
views
Filtering out useful targets for mirna
target
identification
mirna
genes
updated 24 months ago by
Buffo
★ 2.4k • written 24 months ago by
Bhanu
• 0
0
votes
0
replies
420
views
Ribosome binding site
binding
target
RBS
site
ribosome
updated 2.0 years ago by
Pierre Lindenbaum
164k • written 2.0 years ago by
upasana
▴ 20
1
vote
2
replies
620
views
RNA-seq dataset of experiment and control group of TARGET-ALL project in TCGA portal
TARGET
RNA-seq
ALL
TCGA
2.1 years ago by
song83244829
▴ 10
1
vote
4
replies
1.1k
views
How to identify epigenetic complexes and transcription factors targeting list of genes?
Target
RNA-seq
factors
complexes
Epigenetic
2.3 years ago by
ivana.ribarski-chorev
▴ 10
3
votes
4
replies
1.1k
views
data correaltion
correlation
deseq2
prediction
R
target
updated 2.4 years ago by
Michael
55k • written 2.5 years ago by
roniozagam94
▴ 10
0
votes
9
replies
2.0k
views
Haplotype Caller GATK Query
Sequencing
enrichment
Target
GATK-Haplotype-Caller
2.7 years ago by
ramshahaya
▴ 10
0
votes
4
replies
989
views
th way to identification the target genes of enhacners
target
gene
2.7 years ago by
腾纬
• 0
0
votes
2
replies
774
views
how to convert from CpG island methylation array ID to target ID?
symbel
CpG
id
methylation
target
gene
IDs
island
array
2.7 years ago by
xinhui.wang
▴ 560
0
votes
0
replies
480
views
tools for miRNA target prediction in plants
Target
miRNA
updated 16 months ago by
Ram
44k • written 3.0 years ago by
harshraje19
▴ 40
0
votes
0
replies
828
views
Connectivity Map (CMap) Query tool: list of compounds with respective targets given a set of DEGs
CMap
target
DEG
ncs
3.0 years ago by
appropiate
▴ 80
0
votes
0
replies
512
views
KEGG pathway analysis of miRNA in rice(oryza sativa)
target
kegg
pathway
miRNA
prediction
3.3 years ago by
Aswini
• 0
2
votes
1
reply
3.7k
views
Alternatives to DrugBank Database?
target
protein
drug
database
gene
updated 3.7 years ago by
ellimilial
▴ 20 • written 3.7 years ago by
cannin
▴ 350
1
vote
1
reply
1.0k
views
Identification of lncRNA target genes
RNA-Seq
lncRNA
Target
plant
sequencing
3.8 years ago by
Reza
▴ 10
0
votes
4
replies
1.7k
views
Why is the hg38 exome so much bigger than hg19?
hg38
refseq
exome
target
updated 4.5 years ago by
vkkodali_ncbi
★ 3.8k • written 4.5 years ago by
ej
▴ 70
2
votes
2
replies
2.0k
views
ploting a network of mRNAs and miRNAs
miRNA
target
R
updated 4.6 years ago by
Biostar
20 • written 7.6 years ago by
zizigolu
★ 4.3k
0
votes
2
replies
3.7k
views
How To Extract Target Domains/Sequences From Interproscan Tsv Results
target
updated 4.6 years ago by
Biostar
20 • written 10.8 years ago by
chevivien
▴ 90
0
votes
2
replies
1.1k
views
convenient tools to collect target mapping metrics
target
mapping
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
J.F.Jiang
▴ 930
4
votes
2
replies
1.1k
views
a gene become a drug target
drug
target
drug target
updated 4.9 years ago by
Kevin Blighe
88k • written 4.9 years ago by
Shicheng Guo
★ 9.5k
2
votes
1
reply
1.1k
views
Upstream regulators of a gene/protein
TF
Regulation
Target
updated 5.2 years ago by
piyushjo
▴ 710 • written 5.2 years ago by
chipolino
▴ 150
70
votes
12
replies
31k
views
8 follow
Drug to Target/Gene/Protein Interaction Databases
protein
target
database
drug
gene
updated 3.2 years ago by
Ram
44k • written 12.7 years ago by
Wayne
★ 1.0k
2
votes
3
replies
5.2k
views
How To Retrieve Hmmsearch Output Sequences From Target Database..
target
database
updated 6.3 years ago by
michau
▴ 60 • written 10.9 years ago by
chevivien
▴ 90
0
votes
0
replies
1.1k
views
Combined miRNA Target Prediction Algorithms for Custom Datasets/Species
miRNA
target
prediciton
6.4 years ago by
underasail
• 0
7
votes
9
replies
3.5k
views
MicroRNA-target interactions databases
microRNA
Target
Interaction
updated 6.5 years ago by
Björn
▴ 110 • written 6.5 years ago by
Joe Kherery
▴ 140
7
votes
3
replies
2.1k
views
Comprehensive & integrated drug/target database?
drug
target
database
updated 6.6 years ago by
Denise CS
★ 5.2k • written 6.6 years ago by
sam237337
▴ 70
1
vote
4
replies
2.4k
views
How to get a list of all human protein targets and their target class? UniProt or ChEMBL?
ChEMBL
UniProt
Target
6.7 years ago by
Leanna
▴ 10
23
votes
19
replies
7.3k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 19 months ago by
Ram
44k • written 8.1 years ago by
chen
★ 2.5k
1
vote
0
replies
1.3k
views
What is an indirect interaction in a drug-protein interaction database?
drug
target
database
6.8 years ago by
kakukeshi
▴ 80
0
votes
6
replies
2.9k
views
Finding target genes of a TF
RNA-Seq
TF
target
plants
updated 7.1 years ago by
Alex Reynolds
35k • written 7.1 years ago by
hodatn
• 0
1
vote
6
replies
3.8k
views
lncRNA target identification
lncRNA
Target
updated 7.3 years ago by
zhangjunpeng_411
• 0 • written 8.1 years ago by
nazaninhoseinkhan
▴ 530
0
votes
4
replies
3.8k
views
Ngsrich Output Explanation
target
enrichment
updated 7.4 years ago by
Biostar
20 • written 12.4 years ago by
mark.dunning
▴ 230
4
votes
10
replies
4.5k
views
7 follow
An Up-To-Date, Parse-Able And Free Antibody Database
database
target
gene
protein
updated 2.4 years ago by
Ram
44k • written 12.4 years ago by
B. Arman Aksoy
★ 1.2k
0
votes
0
replies
1.2k
views
Threshold for variant detection by Haloplex
Target
7.6 years ago by
jonessara770
▴ 240
5
votes
8
replies
3.2k
views
6 follow
miRNA Target database?
miRNA
miRNA-seq
Target
Database
updated 7.7 years ago by
zizigolu
★ 4.3k • written 7.7 years ago by
Buffo
★ 2.4k
0
votes
0
replies
1.2k
views
Which type of cancer over-expressed my genes
oncology
expression
target
7.8 years ago by
bzhtgb
▴ 10
0
votes
0
replies
5.6k
views
lncRNA target interaction prediction
lncRNA
Target
deltaG
7.9 years ago by
nazaninhoseinkhan
▴ 530
3
votes
2
replies
2.2k
views
TARGET Pediatric Cancer Code Table
TARGET
Code
8.0 years ago by
komal.rathi
★ 4.1k
17
votes
12
replies
25k
views
10 follow
How Can I Find Target Genes Of A Transcription Factor?
target
gene
transcription
updated 2.5 years ago by
Ram
44k • written 12.7 years ago by
Reyhan
▴ 40
6
votes
1
reply
1.8k
views
Type of inhibition between miRNA-mRNA
mirna
plant
target
updated 16 months ago by
Ram
44k • written 8.2 years ago by
Prasad
★ 1.6k
50 results • Page
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Clustering and dynamic tree cutting
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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Answer: Coverage data for TCGA BAM files
RNA-Seq vs DNA-Seq variant calling
C: GSEA error - After pruning, none of the gene sets passed size thresholds
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Answer: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
wangziwei0010
▴ 30
Hi ATpoint, Thank you for your though provoking answer. Big fans! Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs
by
Ming Tommy Tang
★ 4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/ also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session
by
Dunois
★ 2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
Comment: PyDeseq2 - InvalidIndexError
by
Dunois
★ 2.7k
You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra
by
Dunois
★ 2.7k
Expand your search by searching these (two) sequences against other sets of sequences. That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
• 0
I'm wondering if this could work: `bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l` …
Comment: GISTIC 2.0 parameter change not happening
by
Ram
44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data
by
allingt
• 0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
• 0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
• 0
example vcf: ``` CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4 chr1 100 . C …
Comment: Snakemake expand(): using a helper function (zip) and imputing wildcards?
by
Jesse
▴ 850
Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
Comment: Extract significant DEGs using Seurat FindConservedMarkers and FindAllMarkers
by
allingt
• 0
In general, you should threshold on the p value that corresponds to the maximum FDR you can accept. In practice, for scRNA-seq data, many g…
Comment: T cell subtype annotation
by
allingt
• 0
I guess reference-based annotation is not an option? In my experience, visualising the expression of canonical markers (I don't know if CD4…
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